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hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" href="/plots/overview"><div class="mr-4 rounded-md p-1 group-hover:bg-primary zinc-box group-hover:brightness-100 group-hover:ring-0 ring-1 ring-gray-950/5 dark:ring-gray-700/40"><svg class="h-4 w-4 secondary-opacity group-hover:fill-primary-dark group-hover:bg-white bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/duotone/chart-scatter-bubble.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg></div>Plots</a></li><li class="list-none"><a class="pl-4 group flex items-center lg:text-sm lg:leading-6 mb-5 sm:mb-4 font-medium text-gray-600 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" href="/admin/overview"><div class="mr-4 rounded-md p-1 group-hover:bg-primary zinc-box group-hover:brightness-100 group-hover:ring-0 ring-1 ring-gray-950/5 dark:ring-gray-700/40"><svg class="h-4 w-4 secondary-opacity group-hover:fill-primary-dark group-hover:bg-white bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/duotone/screen-users.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg></div>Administration</a></li><li class="list-none"><a class="pl-4 group flex items-center lg:text-sm lg:leading-6 mb-5 sm:mb-4 font-medium text-gray-600 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" href="/resources/faq"><div class="mr-4 rounded-md p-1 group-hover:bg-primary zinc-box group-hover:brightness-100 group-hover:ring-0 ring-1 ring-gray-950/5 dark:ring-gray-700/40"><svg class="h-4 w-4 secondary-opacity group-hover:fill-primary-dark group-hover:bg-white bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/duotone/clipboard-question.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg></div>Resources</a></li><div class="mt-12 lg:mt-8"><h5 class="pl-4 mb-3.5 lg:mb-2.5 font-semibold text-gray-900 dark:text-gray-200">Overview</h5><ul><li id="/workflows/overview" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/overview"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/magnifying-glass.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Workflows & SDK</div></div></a></li></ul></div><div class="mt-12 lg:mt-8"><h5 class="pl-4 mb-3.5 lg:mb-2.5 font-semibold text-gray-900 dark:text-gray-200">Workflows</h5><ul><li><div class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem"><div>Verified Workflows</div><svg width="3" height="24" viewBox="0 -9 3 24" class="transition-transform text-gray-400 overflow-visible group-hover:text-gray-600 dark:text-gray-600 dark:group-hover:text-gray-400 duration-75 rotate-90"><path d="M0 0L3 3L0 6" fill="none" stroke="currentColor" stroke-width="1.5" stroke-linecap="round"></path></svg></div><ul><li><div class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1.75rem"><div>Bulk RNA-seq</div><svg width="3" height="24" viewBox="0 -9 3 24" class="transition-transform text-gray-400 overflow-visible group-hover:text-gray-600 dark:text-gray-600 dark:group-hover:text-gray-400 duration-75 rotate-90"><path d="M0 0L3 3L0 6" fill="none" stroke="currentColor" stroke-width="1.5" stroke-linecap="round"></path></svg></div><ul><li id="/workflows/bulk-rna-seq-deep-dive" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:2.5rem" href="/workflows/bulk-rna-seq-deep-dive"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/flask-gear.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Bulk RNA Seq Overview</div></div></a></li><li id="/workflows/bulk-rna-seq" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg bg-primary/10 text-primary font-semibold dark:text-primary-light dark:bg-primary-light/10" style="padding-left:2.5rem" href="/workflows/bulk-rna-seq"><svg class="h-4 w-4 bg-primary dark:bg-primary-light" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/screwdriver-wrench.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Bulk RNA Seq</div></div></a></li></ul></li><li><div class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1.75rem"><div>ATAC-seq</div><svg width="3" height="24" viewBox="0 -9 3 24" class="transition-transform text-gray-400 overflow-visible group-hover:text-gray-600 dark:text-gray-600 dark:group-hover:text-gray-400"><path d="M0 0L3 3L0 6" fill="none" stroke="currentColor" stroke-width="1.5" stroke-linecap="round"></path></svg></div></li><li id="/workflows/crispresso2" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1.75rem" href="/workflows/crispresso2"><div class="flex-1 flex items-center space-x-2.5"><div>CRISPResso2</div></div></a></li><li id="/workflows/cas-offinder" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1.75rem" href="/workflows/cas-offinder"><div class="flex-1 flex items-center space-x-2.5"><div>CAS-OFFinder</div></div></a></li><li id="/workflows/crispor" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1.75rem" href="/workflows/crispor"><div class="flex-1 flex items-center space-x-2.5"><div>CRISPOR</div></div></a></li><li id="/workflows/alphafold" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1.75rem" href="/workflows/alphafold"><div class="flex-1 flex items-center space-x-2.5"><div>AlphaFold</div></div></a></li><li><div class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1.75rem"><div>MAGeCK</div><svg width="3" height="24" viewBox="0 -9 3 24" class="transition-transform text-gray-400 overflow-visible group-hover:text-gray-600 dark:text-gray-600 dark:group-hover:text-gray-400"><path d="M0 0L3 3L0 6" fill="none" stroke="currentColor" stroke-width="1.5" stroke-linecap="round"></path></svg></div></li></ul></li><li id="/workflows/csv-import" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/csv-import"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/file-import.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>CSV Parameter Import</div></div></a></li><li id="/workflows/resource-monitoring" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/resource-monitoring"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/memory.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Resource Monitoring</div></div></a></li></ul></div><div class="mt-12 lg:mt-8"><h5 class="pl-4 mb-3.5 lg:mb-2.5 font-semibold text-gray-900 dark:text-gray-200">Python SDK</h5><ul><li id="/workflows/sdk/getting-started/quick-start" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/getting-started/quick-start"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/play.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Quick Start</div></div></a></li><li id="/workflows/sdk/getting-started/authorizing-your-own-workflow" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/getting-started/authorizing-your-own-workflow"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/duotone/arrow-progress.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Authoring your Own Workflow</div></div></a></li><li><div class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem"><div>Workflow Concepts</div><svg width="3" height="24" viewBox="0 -9 3 24" class="transition-transform text-gray-400 overflow-visible group-hover:text-gray-600 dark:text-gray-600 dark:group-hover:text-gray-400"><path d="M0 0L3 3L0 6" fill="none" stroke="currentColor" stroke-width="1.5" stroke-linecap="round"></path></svg></div></li><li><div class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem"><div>Testing and Debugging a Workflow</div><svg width="3" height="24" viewBox="0 -9 3 24" class="transition-transform text-gray-400 overflow-visible group-hover:text-gray-600 dark:text-gray-600 dark:group-hover:text-gray-400"><path d="M0 0L3 3L0 6" fill="none" stroke="currentColor" stroke-width="1.5" stroke-linecap="round"></path></svg></div></li></ul></div><div class="mt-12 lg:mt-8"><h5 class="pl-4 mb-3.5 lg:mb-2.5 font-semibold text-gray-900 dark:text-gray-200">Nextflow</h5><ul><li id="/workflows/sdk/nextflow/overview" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/nextflow/overview"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/magnifying-glass.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Overview</div></div></a></li><li id="/workflows/sdk/nextflow/tutorial" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/nextflow/tutorial"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/book.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Tutorial</div></div></a></li><li id="/workflows/sdk/nextflow/profiles" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/nextflow/profiles"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/user.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Execution Profiles</div></div></a></li><li id="/workflows/sdk/nextflow/caching" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/nextflow/caching"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/window-restore.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Caching and Resuming</div></div></a></li><li id="/workflows/sdk/nextflow/registries" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/nextflow/registries"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/lock.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Private Registries</div></div></a></li><li><div class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem"><div>Customizing Your Interface</div><svg width="3" height="24" viewBox="0 -9 3 24" class="transition-transform text-gray-400 overflow-visible group-hover:text-gray-600 dark:text-gray-600 dark:group-hover:text-gray-400"><path d="M0 0L3 3L0 6" fill="none" stroke="currentColor" stroke-width="1.5" stroke-linecap="round"></path></svg></div></li><li id="/workflows/sdk/nextflow/dependencies" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/nextflow/dependencies"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/arrow-progress.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Dependencies</div></div></a></li><li id="/workflows/sdk/nextflow/gpus" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/nextflow/gpus"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/microchip.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Using GPU Accelerators</div></div></a></li></ul></div><div class="mt-12 lg:mt-8"><h5 class="pl-4 mb-3.5 lg:mb-2.5 font-semibold text-gray-900 dark:text-gray-200">Snakemake</h5><ul><li id="/workflows/sdk/snakemake/quickstart" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/snakemake/quickstart"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/play.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Quick Start</div></div></a></li><li id="/workflows/sdk/snakemake/cloud" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/snakemake/cloud"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/cloud.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Snakemake Workflow Cloud Compatibility</div></div></a></li><li><div class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem"><div>Advanced Configuration</div><svg width="3" height="24" viewBox="0 -9 3 24" class="transition-transform text-gray-400 overflow-visible group-hover:text-gray-600 dark:text-gray-600 dark:group-hover:text-gray-400"><path d="M0 0L3 3L0 6" fill="none" stroke="currentColor" stroke-width="1.5" stroke-linecap="round"></path></svg></div></li><li id="/workflows/sdk/snakemake/tutorial" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/snakemake/tutorial"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/book.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Tutorial</div></div></a></li><li id="/workflows/sdk/snakemake/debugging" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/snakemake/debugging"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/bug-slash.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Debugging Snakemake</div></div></a></li><li id="/workflows/sdk/snakemake/troubleshooting" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/snakemake/troubleshooting"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/bugs.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Troubleshooting</div></div></a></li><li id="/workflows/sdk/snakemake/backend" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/snakemake/backend"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/archway.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Architecture Overview</div></div></a></li></ul></div><div class="mt-12 lg:mt-8"><h5 class="pl-4 mb-3.5 lg:mb-2.5 font-semibold text-gray-900 dark:text-gray-200">Automation</h5><ul><li id="/workflows/sdk/automation/overview" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/automation/overview"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/robot.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Workflows Automations</div></div></a></li><li id="/workflows/sdk/automation/example-data-addition" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/automation/example-data-addition"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/table.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Example Data Addition Trigger</div></div></a></li><li id="/workflows/sdk/automation/example-interval" class="scroll-m-4 first:scroll-m-20"><a class="group mt-2 lg:mt-0 flex items-center pr-3 py-1.5 cursor-pointer focus:outline-primary dark:focus:outline-primary-light space-x-3 rounded-lg hover:bg-gray-600/5 dark:hover:bg-gray-200/5 text-gray-700 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300" style="padding-left:1rem" href="/workflows/sdk/automation/example-interval"><svg class="h-4 w-4 bg-gray-400 dark:bg-gray-500" style="-webkit-mask-image:url(https://mintlify.b-cdn.net/v6.6.0/solid/alarm-snooze.svg);-webkit-mask-repeat:no-repeat;-webkit-mask-position:center"></svg><div class="flex-1 flex items-center space-x-2.5"><div>Example Interval Trigger</div></div></a></li></ul></div></div></div></div></div><div class="" id="content-container"><div class="flex flex-row gap-12 box-border w-full pt-40 lg:pt-10"><div class="relative grow box-border flex-col w-full mx-auto px-1 lg:pl-[23.7rem] lg:-ml-12 xl:w-[calc(100%-28rem)]" id="content-area"><header id="header" class="relative"><div class="mt-0.5 space-y-2.5"><div class="eyebrow h-5 text-primary dark:text-primary-light text-sm font-semibold">Bulk RNA-seq</div><div class="flex items-center"><h1 class="inline-block text-2xl sm:text-3xl font-extrabold text-gray-900 tracking-tight dark:text-gray-200">Bulk RNAseq Quantification Walkthrough</h1></div></div></header><div class="flex flex-col gap-8"><div class="flex flex-col gap-6 xl:hidden [&:not(:empty)]:mt-8"></div></div><div class="relative mt-8 prose prose-gray dark:prose-invert"><h2 class="flex whitespace-pre-wrap group" id="upload-your-rnaseq-data"><div class="absolute"><a href="#upload-your-rnaseq-data" class="-ml-10 flex items-center opacity-0 border-0 group-hover:opacity-100" aria-label="Navigate to header"><div class="w-6 h-6 text-gray-400 rounded-md flex items-center justify-center zinc-box bg-white ring-1 ring-gray-400/30 dark:ring-gray-700/25 hover:ring-gray-400/60 dark:hover:ring-white/20"><svg xmlns="http://www.w3.org/2000/svg" fill="gray" height="12px" viewBox="0 0 576 512"><path d="M0 256C0 167.6 71.6 96 160 96h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C98.1 144 48 194.1 48 256s50.1 112 112 112h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C71.6 416 0 344.4 0 256zm576 0c0 88.4-71.6 160-160 160H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c61.9 0 112-50.1 112-112s-50.1-112-112-112H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c88.4 0 160 71.6 160 160zM184 232H392c13.3 0 24 10.7 24 24s-10.7 24-24 24H184c-13.3 0-24-10.7-24-24s10.7-24 24-24z"></path></svg></div></a></div><span class="cursor-pointer">Upload your RNAseq data</span></h2> <div role="list" class="ml-3.5 mt-10 mb-6"><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">1</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Navigate to the Latch Data tab on the left panel.</p><div><p>Use the ‘Upload’ modal found on the top right, and upload your raw .fastq or .fastq.gz files to Latch Data with the upload modal.</p></div></div></div></div> <h3 class="flex whitespace-pre-wrap group" id="set-up-samplesheet-on-latch-registry"><div class="absolute"><a href="#set-up-samplesheet-on-latch-registry" class="-ml-10 flex items-center opacity-0 border-0 group-hover:opacity-100" aria-label="Navigate to header"><div class="w-6 h-6 text-gray-400 rounded-md flex items-center justify-center zinc-box bg-white ring-1 ring-gray-400/30 dark:ring-gray-700/25 hover:ring-gray-400/60 dark:hover:ring-white/20"><svg xmlns="http://www.w3.org/2000/svg" fill="gray" height="12px" viewBox="0 0 576 512"><path d="M0 256C0 167.6 71.6 96 160 96h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C98.1 144 48 194.1 48 256s50.1 112 112 112h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C71.6 416 0 344.4 0 256zm576 0c0 88.4-71.6 160-160 160H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c61.9 0 112-50.1 112-112s-50.1-112-112-112H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c88.4 0 160 71.6 160 160zM184 232H392c13.3 0 24 10.7 24 24s-10.7 24-24 24H184c-13.3 0-24-10.7-24-24s10.7-24 24-24z"></path></svg></div></a></div><span class="cursor-pointer">Set up samplesheet on Latch Registry</span></h3> <div role="list" class="ml-3.5 mt-10 mb-6"><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">1</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Navigate to the Latch Registry tab on the left panel.</p><div><p>Create new Project (if needed) and a new Sheet under that Project for the experiment being run.</p></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">2</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Select the ‘Import -> Bulk Import Sequencing Data’ modal on the top right of the screen.</p><div></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">3</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Choose the folder containing your raw RNAseq data and click ‘Select’.</p><div></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">4</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Confirm or modify name parsing method used to auto-group your samples and click ‘Next’.</p><div></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">5</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Fill in ‘fastq_1’ and ‘fastq_2’ for your forward and reverse read file respectively and click ‘Import’.</p><div></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-transparent bg-gradient-to-b from-gray-200 dark:from-white/10 via-80% to-transparent"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">6</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">This will generate a samplesheet on Latch Registry for your data.</p><div></div></div></div></div> <h3 class="flex whitespace-pre-wrap group" id="launch-nf-core-rnaseq-latch-workflow"><div class="absolute"><a href="#launch-nf-core-rnaseq-latch-workflow" class="-ml-10 flex items-center opacity-0 border-0 group-hover:opacity-100" aria-label="Navigate to header"><div class="w-6 h-6 text-gray-400 rounded-md flex items-center justify-center zinc-box bg-white ring-1 ring-gray-400/30 dark:ring-gray-700/25 hover:ring-gray-400/60 dark:hover:ring-white/20"><svg xmlns="http://www.w3.org/2000/svg" fill="gray" height="12px" viewBox="0 0 576 512"><path d="M0 256C0 167.6 71.6 96 160 96h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C98.1 144 48 194.1 48 256s50.1 112 112 112h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C71.6 416 0 344.4 0 256zm576 0c0 88.4-71.6 160-160 160H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c61.9 0 112-50.1 112-112s-50.1-112-112-112H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c88.4 0 160 71.6 160 160zM184 232H392c13.3 0 24 10.7 24 24s-10.7 24-24 24H184c-13.3 0-24-10.7-24-24s10.7-24 24-24z"></path></svg></div></a></div><span class="cursor-pointer">Launch ‘nf-core/rnaseq’ Latch Workflow</span></h3> <div role="list" class="ml-3.5 mt-10 mb-6"><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">1</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Navigate to the Latch Workflows tab on the left panel.</p><div><p>Choose the ‘nf-core/rnaseq’ workflow in ‘All Workflows’ or My Workflows’ (if you have added it).</p></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">2</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Import samplesheet with ‘Import Rows from Registry’.</p><div></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">3</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Choose needed samplesheet, followed by needed samples (select all on top left if needed.</p><div></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">4</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Map samplesheet columns to workflow parameters and click ‘Import’.</p><div><div class="my-4 px-5 py-4 overflow-hidden rounded-xl flex gap-3 border border-sky-500/20 bg-sky-50/50 dark:border-sky-500/30 dark:bg-sky-500/10"><div class="mt-0.5 w-4"><svg width="14" height="14" viewBox="0 0 14 14" fill="currentColor" xmlns="http://www.w3.org/2000/svg" class="w-4 h-4 text-sky-500" aria-label="Note"><path fill-rule="evenodd" clip-rule="evenodd" d="M7 1.3C10.14 1.3 12.7 3.86 12.7 7C12.7 10.14 10.14 12.7 7 12.7C5.48908 12.6974 4.0408 12.096 2.97241 11.0276C1.90403 9.9592 1.30264 8.51092 1.3 7C1.3 3.86 3.86 1.3 7 1.3ZM7 0C3.14 0 0 3.14 0 7C0 10.86 3.14 14 7 14C10.86 14 14 10.86 14 7C14 3.14 10.86 0 7 0ZM8 3H6V8H8V3ZM8 9H6V11H8V9Z"></path></svg></div><div class="text-sm prose min-w-0 text-sky-900 dark:text-sky-200">Click on the (x) for strandedness in most cases - only use strandedness if you have an nf-core specific strandedness column in your metadata.</div></div></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">5</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Choose ‘Reference Genome’ from ‘Latch Verified Reference Genome’ tab.</p><div><p>Or choose your own Reference FASTA and GTF in the ‘Custom Reference Genome’ tab.</p></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">6</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">[Optional - Advanced] Choose alignment method or pseudoalignment method.</p><div></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">7</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">[Fill in a ‘Run Name’ and hit ‘Launch Execution’.</p><div><p>Do not use spaces in the Run Name.</p><div class="my-4 px-5 py-4 overflow-hidden rounded-xl flex gap-3 border border-sky-500/20 bg-sky-50/50 dark:border-sky-500/30 dark:bg-sky-500/10"><div class="mt-0.5 w-4"><svg width="14" height="14" viewBox="0 0 14 14" fill="currentColor" xmlns="http://www.w3.org/2000/svg" class="w-4 h-4 text-sky-500" aria-label="Note"><path fill-rule="evenodd" clip-rule="evenodd" d="M7 1.3C10.14 1.3 12.7 3.86 12.7 7C12.7 10.14 10.14 12.7 7 12.7C5.48908 12.6974 4.0408 12.096 2.97241 11.0276C1.90403 9.9592 1.30264 8.51092 1.3 7C1.3 3.86 3.86 1.3 7 1.3ZM7 0C3.14 0 0 3.14 0 7C0 10.86 3.14 14 7 14C10.86 14 14 10.86 14 7C14 3.14 10.86 0 7 0ZM8 3H6V8H8V3ZM8 9H6V11H8V9Z"></path></svg></div><div class="text-sm prose min-w-0 text-sky-900 dark:text-sky-200">We recommend leaving the Output Directory to its default location.</div></div><p>(Optional - Advanced) Choose other parameters in ‘Optional Arguments’. <div class="my-4 px-5 py-4 overflow-hidden rounded-xl flex gap-3 border border-sky-500/20 bg-sky-50/50 dark:border-sky-500/30 dark:bg-sky-500/10"><div class="mt-0.5 w-4"><svg width="14" height="14" viewBox="0 0 14 14" fill="currentColor" xmlns="http://www.w3.org/2000/svg" class="w-4 h-4 text-sky-500" aria-label="Note"><path fill-rule="evenodd" clip-rule="evenodd" d="M7 1.3C10.14 1.3 12.7 3.86 12.7 7C12.7 10.14 10.14 12.7 7 12.7C5.48908 12.6974 4.0408 12.096 2.97241 11.0276C1.90403 9.9592 1.30264 8.51092 1.3 7C1.3 3.86 3.86 1.3 7 1.3ZM7 0C3.14 0 0 3.14 0 7C0 10.86 3.14 14 7 14C10.86 14 14 10.86 14 7C14 3.14 10.86 0 7 0ZM8 3H6V8H8V3ZM8 9H6V11H8V9Z"></path></svg></div><div class="text-sm prose min-w-0 text-sky-900 dark:text-sky-200">There are descriptions for every parameter available when you hover above the (i) symbol on a parameter name.</div></div></p></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">8</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">[Optional] Monitor the execution under ‘All Executions’.</p><div><p>Double click the execution to be taken to detailed logs.</p></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-transparent bg-gradient-to-b from-gray-200 dark:from-white/10 via-80% to-transparent"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">9</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Once complete, the output will be found in the output directory under your provided run name.</p><div><p>Useful outputs are the run HTML report and all the computational outputs in the folder that matches the name of the aligner you used.</p></div></div></div></div> <h2 class="flex whitespace-pre-wrap group" id="differential-gene-expression"><div class="absolute"><a href="#differential-gene-expression" class="-ml-10 flex items-center opacity-0 border-0 group-hover:opacity-100" aria-label="Navigate to header"><div class="w-6 h-6 text-gray-400 rounded-md flex items-center justify-center zinc-box bg-white ring-1 ring-gray-400/30 dark:ring-gray-700/25 hover:ring-gray-400/60 dark:hover:ring-white/20"><svg xmlns="http://www.w3.org/2000/svg" fill="gray" height="12px" viewBox="0 0 576 512"><path d="M0 256C0 167.6 71.6 96 160 96h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C98.1 144 48 194.1 48 256s50.1 112 112 112h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C71.6 416 0 344.4 0 256zm576 0c0 88.4-71.6 160-160 160H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c61.9 0 112-50.1 112-112s-50.1-112-112-112H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c88.4 0 160 71.6 160 160zM184 232H392c13.3 0 24 10.7 24 24s-10.7 24-24 24H184c-13.3 0-24-10.7-24-24s10.7-24 24-24z"></path></svg></div></a></div><span class="cursor-pointer">Differential Gene Expression</span></h2> <h3 class="flex whitespace-pre-wrap group" id="launch-deseq2-differential-expression-latch-workflow"><div class="absolute"><a href="#launch-deseq2-differential-expression-latch-workflow" class="-ml-10 flex items-center opacity-0 border-0 group-hover:opacity-100" aria-label="Navigate to header"><div class="w-6 h-6 text-gray-400 rounded-md flex items-center justify-center zinc-box bg-white ring-1 ring-gray-400/30 dark:ring-gray-700/25 hover:ring-gray-400/60 dark:hover:ring-white/20"><svg xmlns="http://www.w3.org/2000/svg" fill="gray" height="12px" viewBox="0 0 576 512"><path d="M0 256C0 167.6 71.6 96 160 96h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C98.1 144 48 194.1 48 256s50.1 112 112 112h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C71.6 416 0 344.4 0 256zm576 0c0 88.4-71.6 160-160 160H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c61.9 0 112-50.1 112-112s-50.1-112-112-112H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c88.4 0 160 71.6 160 160zM184 232H392c13.3 0 24 10.7 24 24s-10.7 24-24 24H184c-13.3 0-24-10.7-24-24s10.7-24 24-24z"></path></svg></div></a></div><span class="cursor-pointer">Launch ‘DESeq2 (Differential Expression)’ Latch Workflow</span></h3> <div role="list" class="ml-3.5 mt-10 mb-6"><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">1</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Navigate to the Latch Workflows tab on the left panel.</p><div><p>Choose the ‘DESeq2 (Differential Expression)’ workflow in ‘All Workflows’ or My Workflows’ (if you have added it).</p></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">2</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Choose your input counts file from the outputs of ‘nf-core/rnaseq’.</p><div><div class="my-4 px-5 py-4 overflow-hidden rounded-xl flex gap-3 border border-sky-500/20 bg-sky-50/50 dark:border-sky-500/30 dark:bg-sky-500/10"><div class="mt-0.5 w-4"><svg width="14" height="14" viewBox="0 0 14 14" fill="currentColor" xmlns="http://www.w3.org/2000/svg" class="w-4 h-4 text-sky-500" aria-label="Note"><path fill-rule="evenodd" clip-rule="evenodd" d="M7 1.3C10.14 1.3 12.7 3.86 12.7 7C12.7 10.14 10.14 12.7 7 12.7C5.48908 12.6974 4.0408 12.096 2.97241 11.0276C1.90403 9.9592 1.30264 8.51092 1.3 7C1.3 3.86 3.86 1.3 7 1.3ZM7 0C3.14 0 0 3.14 0 7C0 10.86 3.14 14 7 14C10.86 14 14 10.86 14 7C14 3.14 10.86 0 7 0ZM8 3H6V8H8V3ZM8 9H6V11H8V9Z"></path></svg></div><div class="text-sm prose min-w-0 text-sky-900 dark:text-sky-200">All outputs from ‘nf-core/rnaseq’ have an output folder called ‘deseq2_counts’ with a TSV file that is the optimal input for DESeq2.</div></div></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">3</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Choose your conditions for your samples in the ‘Manual Input’ design matrix tab.</p><div><p>Or choose advanced conditions for your samples in the ‘File/Registry’ tab through Latch Data or Latch Registry.</p></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-transparent bg-gradient-to-b from-gray-200 dark:from-white/10 via-80% to-transparent"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">4</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Choose ‘Report Name’ and hit ‘Launch Workflow’.</p><div><div class="my-4 px-5 py-4 overflow-hidden rounded-xl flex gap-3 border border-sky-500/20 bg-sky-50/50 dark:border-sky-500/30 dark:bg-sky-500/10"><div class="mt-0.5 w-4"><svg width="14" height="14" viewBox="0 0 14 14" fill="currentColor" xmlns="http://www.w3.org/2000/svg" class="w-4 h-4 text-sky-500" aria-label="Note"><path fill-rule="evenodd" clip-rule="evenodd" d="M7 1.3C10.14 1.3 12.7 3.86 12.7 7C12.7 10.14 10.14 12.7 7 12.7C5.48908 12.6974 4.0408 12.096 2.97241 11.0276C1.90403 9.9592 1.30264 8.51092 1.3 7C1.3 3.86 3.86 1.3 7 1.3ZM7 0C3.14 0 0 3.14 0 7C0 10.86 3.14 14 7 14C10.86 14 14 10.86 14 7C14 3.14 10.86 0 7 0ZM8 3H6V8H8V3ZM8 9H6V11H8V9Z"></path></svg></div><div class="text-sm prose min-w-0 text-sky-900 dark:text-sky-200">We recommend leaving the Output to its default location.</div></div></div></div></div></div> <h3 class="flex whitespace-pre-wrap group" id="visualize-differential-gene-expression-outputs-in-latch-plots"><div class="absolute"><a href="#visualize-differential-gene-expression-outputs-in-latch-plots" class="-ml-10 flex items-center opacity-0 border-0 group-hover:opacity-100" aria-label="Navigate to header"><div class="w-6 h-6 text-gray-400 rounded-md flex items-center justify-center zinc-box bg-white ring-1 ring-gray-400/30 dark:ring-gray-700/25 hover:ring-gray-400/60 dark:hover:ring-white/20"><svg xmlns="http://www.w3.org/2000/svg" fill="gray" height="12px" viewBox="0 0 576 512"><path d="M0 256C0 167.6 71.6 96 160 96h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C98.1 144 48 194.1 48 256s50.1 112 112 112h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C71.6 416 0 344.4 0 256zm576 0c0 88.4-71.6 160-160 160H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c61.9 0 112-50.1 112-112s-50.1-112-112-112H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c88.4 0 160 71.6 160 160zM184 232H392c13.3 0 24 10.7 24 24s-10.7 24-24 24H184c-13.3 0-24-10.7-24-24s10.7-24 24-24z"></path></svg></div></a></div><span class="cursor-pointer">Visualize differential gene expression outputs in Latch Plots</span></h3> <div role="list" class="ml-3.5 mt-10 mb-6"><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">1</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Navigate to the Latch Plots tab on the left panel.</p><div><p>Choose the ‘Differential Gene Expression Visualizer (0.0.6)’ template.</p></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">2</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Once the DESeq2 run is done, choose your outputted run (or select from Latch Data if a custom output location was used) and scroll through for QC graphs and heatmaps.</p><div></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">3</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Choose ‘Contrast Conditions’ and ‘Genes of Interest’ for comparison and visualize Volcano and MA Plots.</p><div></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-transparent bg-gradient-to-b from-gray-200 dark:from-white/10 via-80% to-transparent"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">4</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">If needed, turn on ‘Dev Mode’ in the top right and add more plots or code blocks <Redirect to Plots Wiki>.</p><div><div class="my-4 px-5 py-4 overflow-hidden rounded-xl flex gap-3 border border-sky-500/20 bg-sky-50/50 dark:border-sky-500/30 dark:bg-sky-500/10"><div class="mt-0.5 w-4"><svg width="14" height="14" viewBox="0 0 14 14" fill="currentColor" xmlns="http://www.w3.org/2000/svg" class="w-4 h-4 text-sky-500" aria-label="Note"><path fill-rule="evenodd" clip-rule="evenodd" d="M7 1.3C10.14 1.3 12.7 3.86 12.7 7C12.7 10.14 10.14 12.7 7 12.7C5.48908 12.6974 4.0408 12.096 2.97241 11.0276C1.90403 9.9592 1.30264 8.51092 1.3 7C1.3 3.86 3.86 1.3 7 1.3ZM7 0C3.14 0 0 3.14 0 7C0 10.86 3.14 14 7 14C10.86 14 14 10.86 14 7C14 3.14 10.86 0 7 0ZM8 3H6V8H8V3ZM8 9H6V11H8V9Z"></path></svg></div><div class="text-sm prose min-w-0 text-sky-900 dark:text-sky-200">Click on the (x) for strandedness in most cases - only use strandedness if you have an nf-core specific strandedness column in your metadata.</div></div></div></div></div></div> <h2 class="flex whitespace-pre-wrap group" id="pathway-enrichment"><div class="absolute"><a href="#pathway-enrichment" class="-ml-10 flex items-center opacity-0 border-0 group-hover:opacity-100" aria-label="Navigate to header"><div class="w-6 h-6 text-gray-400 rounded-md flex items-center justify-center zinc-box bg-white ring-1 ring-gray-400/30 dark:ring-gray-700/25 hover:ring-gray-400/60 dark:hover:ring-white/20"><svg xmlns="http://www.w3.org/2000/svg" fill="gray" height="12px" viewBox="0 0 576 512"><path d="M0 256C0 167.6 71.6 96 160 96h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C98.1 144 48 194.1 48 256s50.1 112 112 112h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C71.6 416 0 344.4 0 256zm576 0c0 88.4-71.6 160-160 160H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c61.9 0 112-50.1 112-112s-50.1-112-112-112H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c88.4 0 160 71.6 160 160zM184 232H392c13.3 0 24 10.7 24 24s-10.7 24-24 24H184c-13.3 0-24-10.7-24-24s10.7-24 24-24z"></path></svg></div></a></div><span class="cursor-pointer">Pathway Enrichment</span></h2> <h3 class="flex whitespace-pre-wrap group" id="launch-pathway-enrichment-analysis-latch-workflow"><div class="absolute"><a href="#launch-pathway-enrichment-analysis-latch-workflow" class="-ml-10 flex items-center opacity-0 border-0 group-hover:opacity-100" aria-label="Navigate to header"><div class="w-6 h-6 text-gray-400 rounded-md flex items-center justify-center zinc-box bg-white ring-1 ring-gray-400/30 dark:ring-gray-700/25 hover:ring-gray-400/60 dark:hover:ring-white/20"><svg xmlns="http://www.w3.org/2000/svg" fill="gray" height="12px" viewBox="0 0 576 512"><path d="M0 256C0 167.6 71.6 96 160 96h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C98.1 144 48 194.1 48 256s50.1 112 112 112h72c13.3 0 24 10.7 24 24s-10.7 24-24 24H160C71.6 416 0 344.4 0 256zm576 0c0 88.4-71.6 160-160 160H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c61.9 0 112-50.1 112-112s-50.1-112-112-112H344c-13.3 0-24-10.7-24-24s10.7-24 24-24h72c88.4 0 160 71.6 160 160zM184 232H392c13.3 0 24 10.7 24 24s-10.7 24-24 24H184c-13.3 0-24-10.7-24-24s10.7-24 24-24z"></path></svg></div></a></div><span class="cursor-pointer">Launch ‘Pathway Enrichment Analysis’ Latch Workflow</span></h3> <div role="list" class="ml-3.5 mt-10 mb-6"><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">1</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Navigate to the Latch Workflows tab on the left panel.</p><div><p>Choose the ‘Pathway Enrichment Analysis’ workflow in ‘All Workflows’ or My Workflows’ (if you have added it).</p></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">2</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Choose your needed contrast file from the DESeq2 run output.</p><div><p>Each run will have a ‘Data/Contrast’ folder with a file for every comparison created in DESeq2.</p></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-gray-200/70 dark:bg-white/10"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">3</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200">Choose your ‘Species’ and ‘Run Name’ and hit ‘Launch Workflow’.</p><div></div></div></div><div role="listitem" class="relative flex items-start pb-2"><div class="absolute w-px h-[calc(100%-2.75rem)] top-[2.75rem] bg-transparent bg-gradient-to-b from-gray-200 dark:from-white/10 via-80% to-transparent"></div><div class="absolute ml-[-14px] py-2"><div class="w-7 h-7 shrink-0 rounded-lg bg-gray-100 dark:text-white dark:bg-[#26292E] text-sm text-gray-800 font-semibold flex items-center justify-center">4</div></div><div class="w-full overflow-hidden pl-12 pr-px"><p class="mt-2 font-semibold prose dark:prose-invert text-gray-900 dark:text-gray-200"> Useful outputs are the final ‘Report.html’ generated.</p><div><iframe width="560" height="315" src="https://www.youtube.com/embed/-z7Zb06EM_Y" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture"></iframe></div></div></div></div> <br/> <br/> <a class="card block not-prose font-normal group relative my-2 ring-2 ring-transparent rounded-xl bg-white dark:bg-background-dark border border-gray-950/10 dark:border-white/10 overflow-hidden w-full cursor-pointer hover:!border-primary dark:hover:!border-primary-light" href="/workflows/bulk-rna-seq-deep-dive"><div class="px-6 py-5"><div class="h-6 w-6 fill-gray-800 dark:fill-gray-100 text-gray-800 dark:text-gray-100"><svg width="24" height="24" viewBox="0 0 24 24" fill="none" xmlns="http://www.w3.org/2000/svg"><path fill-rule="evenodd" clip-rule="evenodd" d="M15.7433 2.66893C16.1128 2.2584 16.0795 1.62611 15.6689 1.25668C15.2584 0.887241 14.6261 0.920555 14.2567 1.33109C12.3062 3.49856 11.516 5.68827 11.2033 7.84985C11.1242 8.39645 11.5033 8.90365 12.0499 8.98271C12.4718 9.04374 12.8702 8.83183 13.0664 8.4806L13.2929 8.70711C13.6834 9.09763 14.3166 9.09763 14.7071 8.70711C15.0976 8.31658 15.0976 7.68342 14.7071 7.29289L13.7071 6.29289C13.6817 6.26746 13.6552 6.24369 13.6279 6.22158C13.7974 5.71485 14.0132 5.20898 14.2886 4.7028L16.2929 6.70711C16.6834 7.09763 17.3166 7.09763 17.7071 6.70711C18.0976 6.31658 18.0976 5.68342 17.7071 5.29289L15.437 3.02275C15.5351 2.9049 15.6371 2.78697 15.7433 2.66893ZM22.7433 8.33106C23.1128 8.74158 23.0795 9.37387 22.669 9.74332C19.0499 13.0003 15.3804 13.0001 12.0619 13L12 13C10.7696 13 9.58797 13.0028 8.43455 13.1435C8.57049 13.5004 8.49468 13.9195 8.20711 14.2071C7.81659 14.5976 7.18342 14.5976 6.7929 14.2071L6.21542 13.6296C5.70875 13.7993 5.20506 14.0148 4.70249 14.2883L4.70711 14.2929C5.09764 14.6834 5.09764 15.3166 4.70711 15.7071C4.31659 16.0976 3.68343 16.0976 3.2929 15.7071L3.02272 15.4369C2.90486 15.5351 2.78695 15.6371 2.66895 15.7433C2.25844 16.1128 1.62615 16.0795 1.2567 15.669C0.887249 15.2584 0.920543 14.6261 1.33106 14.2567C4.95008 10.9997 8.61965 10.9999 11.9381 11L12 11C13.2304 11 14.412 10.9972 15.5655 10.8565C15.4295 10.4996 15.5053 10.0805 15.7929 9.79289C16.1834 9.40237 16.8166 9.40237 17.2071 9.79289L17.7846 10.3704C18.2913 10.2007 18.795 9.98524 19.2975 9.71174L19.2929 9.70711C18.9024 9.31658 18.9024 8.68342 19.2929 8.29289C19.6834 7.90237 20.3166 7.90237 20.7071 8.29289L20.9773 8.56308C21.0952 8.46496 21.2131 8.36288 21.3311 8.2567C21.7416 7.88725 22.3739 7.92054 22.7433 8.33106ZM11.9502 15.0173C12.4968 15.0964 12.8758 15.6036 12.7967 16.1502C12.484 18.3117 11.6938 20.5014 9.74334 22.6689C9.3739 23.0795 8.74162 23.1128 8.33109 22.7433C7.92055 22.3739 7.88724 21.7416 8.25668 21.3311C8.3629 21.213 8.46497 21.0951 8.56305 20.9773L6.2929 18.7071C5.90238 18.3166 5.90238 17.6834 6.2929 17.2929C6.68342 16.9024 7.31659 16.9024 7.70711 17.2929L9.71142 19.2972C9.98574 18.793 10.201 18.2891 10.3702 17.7844L9.2929 16.7071C8.90238 16.3166 8.90238 15.6834 9.2929 15.2929C9.68342 14.9024 10.3166 14.9024 10.7071 15.2929L10.9336 15.5194C11.1298 15.1682 11.5282 14.9563 11.9502 15.0173ZM2.50001 5C2.50001 3.34315 3.84315 2 5.50001 2H9.50001C10.0523 2 10.5 2.44772 10.5 3C10.5 3.55228 10.0523 4 9.50001 4H5.50001C4.94772 4 4.50001 4.44772 4.50001 5V9.5C4.50001 10.0523 4.05229 10.5 3.50001 10.5C2.94772 10.5 2.50001 10.0523 2.50001 9.5V5ZM19 22C20.6569 22 22 20.6569 22 19V14.5C22 13.9477 21.5523 13.5 21 13.5C20.4477 13.5 20 13.9477 20 14.5V19C20 19.5523 19.5523 20 19 20H14.5C13.9477 20 13.5 20.4477 13.5 21C13.5 21.5523 13.9477 22 14.5 22H19Z" fill="#4B7AF9"></path></svg></div><div><h2 class="font-semibold text-base text-gray-800 dark:text-white mt-4">Bulk RNA-seq Overview</h2><div class="mt-1 font-normal text-sm leading-6 text-gray-600 dark:text-gray-400"><p>For a detailed overview of how Bulk-RNA Seq works, read our article.</p></div></div></div></a></div><div class="leading-6 mt-14"><div class="pb-16 w-full"><div class="flex flex-col gap-y-4 xl:flex-col xl:gap-6 min-[1400px]:flex-row md:flex-row md:justify-end"><div class="flex flex-row gap-5 items-center grow 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3.45616L10.0437 4.08116C9.86562 4.70304 9.58437 5.29054 9.2125 5.81554C9.05 6.04366 9.03125 6.34366 9.15938 6.59366C9.2875 6.84366 9.54375 6.99991 9.825 6.99991H14C14.275 6.99991 14.5 7.22491 14.5 7.49991C14.5 7.71241 14.3656 7.89679 14.175 7.96866C13.9438 8.05616 13.7688 8.24992 13.7094 8.49054C13.65 8.73117 13.7125 8.98429 13.875 9.16866C13.9531 9.25616 14 9.37179 14 9.49991C14 9.74366 13.825 9.94679 13.5938 9.99054C13.3375 10.0405 13.1219 10.2187 13.0312 10.4624C12.9406 10.7062 12.9813 10.9843 13.1438 11.1905C13.2094 11.2749 13.25 11.3812 13.25 11.4999C13.25 11.7093 13.1187 11.8937 12.9312 11.9655C12.5719 12.1062 12.3781 12.4937 12.4812 12.8655C12.4937 12.9062 12.5 12.953 12.5 12.9999C12.5 13.2749 12.275 13.4999 12 13.4999H8.95312C8.55937 13.4999 8.17188 13.3843 7.84375 13.1655L5.91563 11.8812C5.57188 11.6499 5.10625 11.7437 4.875 12.0905C4.64375 12.4374 4.7375 12.8999 5.08437 13.1312L7.0125 14.4155C7.5875 14.7999 8.2625 15.003 8.95312 15.003H12C13.0844 15.003 13.9656 14.1405 14 13.0655C14.4563 12.6999 14.75 12.1374 14.75 11.503C14.75 11.3624 14.7344 11.228 14.7094 11.0968C15.1906 10.7312 15.5 10.153 15.5 9.50304C15.5 9.29991 15.4688 9.10304 15.4125 8.91866C15.775 8.55304 16 8.05304 16 7.49991C16 6.39679 15.1063 5.49991 14 5.49991H11.1156C11.2625 5.17491 11.3875 4.83741 11.4844 4.49366L11.6625 3.86866C12.0031 2.67491 11.3125 1.42804 10.1187 1.08741ZM1 5.99991C0.446875 5.99991 0 6.44679 0 6.99991V13.9999C0 14.553 0.446875 14.9999 1 14.9999H3C3.55313 14.9999 4 14.553 4 13.9999V6.99991C4 6.44679 3.55313 5.99991 3 5.99991H1Z"></path></svg><small class="text-sm font-normal leading-4 ">Yes</small></button><button class="px-[14px] py-2 flex flex-row gap-[10px] items-center border rounded-lg text-gray-600 dark:text-gray-400 hover:text-gray-700 dark:hover:text-gray-300 bg-white/50 border-gray-200 dark:border-gray-800 dark:bg-codeblock/50 hover:border-gray-400 hover:dark:border-gray-500"><svg xmlns="http://www.w3.org/2000/svg" width="16" height="16" viewBox="0 0 16 16" 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12.9312 4.03115C12.5719 3.89053 12.3781 3.50303 12.4812 3.13115C12.4937 3.09053 12.5 3.04365 12.5 2.99678C12.5 2.72178 12.275 2.49678 12 2.49678H8.95312C8.55937 2.49678 8.17188 2.6124 7.84375 2.83115L5.91563 4.11553C5.57188 4.34678 5.10625 4.25303 4.875 3.90615C4.64375 3.55928 4.7375 3.09678 5.08437 2.86553L7.0125 1.58115C7.5875 1.19678 8.2625 0.993652 8.95312 0.993652H12C13.0844 0.993652 13.9656 1.85615 14 2.93115C14.4563 3.29678 14.75 3.85928 14.75 4.49365C14.75 4.63428 14.7344 4.76865 14.7094 4.8999C15.1906 5.26553 15.5 5.84365 15.5 6.49365C15.5 6.69678 15.4688 6.89365 15.4125 7.07803C15.775 7.44678 16 7.94678 16 8.4999C16 9.60303 15.1063 10.4999 14 10.4999H11.1156C11.2625 10.8249 11.3875 11.1624 11.4844 11.5062L11.6625 12.1312C12.0031 13.3249 11.3125 14.5718 10.1187 14.9124ZM1 11.9999C0.446875 11.9999 0 11.553 0 10.9999V3.9999C0 3.44678 0.446875 2.9999 1 2.9999H3C3.55313 2.9999 4 3.44678 4 3.9999V10.9999C4 11.553 3.55313 11.9999 3 11.9999H1Z"></path></svg><small class="text-sm font-normal leading-4 ">No</small></button></div></div><div class="flex flex-row gap-3 justify-end"></div></div></div><div class="mb-12 px-0.5 flex items-center text-sm font-semibold text-gray-700 dark:text-gray-200"><a class="flex items-center space-x-3 group" href="/workflows/bulk-rna-seq-deep-dive"><svg viewBox="0 0 3 6" class="h-1.5 stroke-gray-400 overflow-visible group-hover:stroke-gray-600 dark:group-hover:stroke-gray-300"><path d="M3 0L0 3L3 6" fill="none" stroke-width="2" stroke-linecap="round" stroke-linejoin="round"></path></svg><span class="group-hover:text-gray-900 dark:group-hover:text-white">Bulk RNA Seq Overview</span></a><a class="flex items-center ml-auto space-x-3 group" href="/workflows/ATAC-Seq-Deep-Dive"><span class="group-hover:text-gray-900 dark:group-hover:text-white">ATAC Seq Overview</span><svg viewBox="0 0 3 6" class="rotate-180 h-1.5 stroke-gray-400 overflow-visible group-hover:stroke-gray-600 dark:group-hover:stroke-gray-300"><path d="M3 0L0 3L3 6" 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class="sm:flex"><a href="https://mintlify.com/preview-request?utm_campaign=poweredBy&utm_medium=docs&utm_source=wiki.latch.bio" target="_blank" rel="noreferrer" class="text-sm text-gray-500 dark:text-gray-400 hover:text-gray-700 dark:hover:text-gray-300">Powered by Mintlify</a></div></div></footer></div></div><div class="z-10 hidden xl:flex pl-10 box-border w-[19rem]" id="table-of-contents"><div id="table-of-contents-content" class="fixed text-gray-600 text-sm leading-6 w-[16.5rem] overflow-y-auto space-y-2 h-[calc(100%-10rem)]"><div class="text-gray-700 dark:text-gray-300 font-medium flex items-center space-x-2"><svg width="16" height="16" viewBox="0 0 16 16" fill="none" stroke="currentColor" stroke-width="2" xmlns="http://www.w3.org/2000/svg" class="h-3 w-3"><path d="M2.44434 12.6665H13.5554" stroke-linecap="round" stroke-linejoin="round"></path><path d="M2.44434 3.3335H13.5554" stroke-linecap="round" stroke-linejoin="round"></path><path d="M2.44434 8H7.33323" stroke-linecap="round" stroke-linejoin="round"></path></svg><span>On this page</span></div><ul><li><a href="#upload-your-rnaseq-data" class="py-1 block font-medium hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300">Upload your RNAseq data</a></li><li style="margin-left:1rem"><a href="#set-up-samplesheet-on-latch-registry" class="group flex items-start py-1 whitespace-pre-wrap text-gray-500 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300">Set up samplesheet on Latch Registry</a></li><li style="margin-left:1rem"><a href="#launch-nf-core-rnaseq-latch-workflow" class="group flex items-start py-1 whitespace-pre-wrap text-gray-500 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300">Launch ‘nf-core/rnaseq’ Latch Workflow</a></li><li><a href="#differential-gene-expression" class="py-1 block font-medium hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300">Differential Gene Expression</a></li><li style="margin-left:1rem"><a href="#launch-deseq2-differential-expression-latch-workflow" class="group flex items-start py-1 whitespace-pre-wrap text-gray-500 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300">Launch ‘DESeq2 (Differential Expression)’ Latch Workflow</a></li><li style="margin-left:1rem"><a href="#visualize-differential-gene-expression-outputs-in-latch-plots" class="group flex items-start py-1 whitespace-pre-wrap text-gray-500 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300">Visualize differential gene expression outputs in Latch Plots</a></li><li><a href="#pathway-enrichment" class="py-1 block font-medium hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300">Pathway Enrichment</a></li><li style="margin-left:1rem"><a href="#launch-pathway-enrichment-analysis-latch-workflow" class="group flex items-start py-1 whitespace-pre-wrap text-gray-500 hover:text-gray-900 dark:text-gray-400 dark:hover:text-gray-300">Launch ‘Pathway Enrichment Analysis’ Latch Workflow</a></li></ul></div></div></div></div></div></div></main></div><script id="__NEXT_DATA__" type="application/json">{"props":{"pageProps":{"mdxSource":{"compiledSource":"/*@jsxRuntime automatic @jsxImportSource react*/\nconst {Fragment: _Fragment, jsx: _jsx, jsxs: _jsxs} = arguments[0];\nconst {useMDXComponents: _provideComponents} = arguments[0];\nfunction _createMdxContent(props) {\n const _components = Object.assign({\n p: \"p\",\n svg: \"svg\",\n path: \"path\"\n }, _provideComponents(), props.components), {Heading, Steps, Step, ZoomImage, Note, Card} = _components;\n if (!Card) _missingMdxReference(\"Card\", true);\n if (!Heading) _missingMdxReference(\"Heading\", true);\n if (!Note) _missingMdxReference(\"Note\", true);\n if (!Step) _missingMdxReference(\"Step\", true);\n if (!Steps) _missingMdxReference(\"Steps\", true);\n if (!ZoomImage) _missingMdxReference(\"ZoomImage\", true);\n return _jsxs(_Fragment, {\n children: [_jsx(Heading, {\n level: \"2\",\n id: \"upload-your-rnaseq-data\",\n children: \"Upload your RNAseq data\"\n }), \"\\n\", _jsx(Steps, {\n children: _jsxs(Step, {\n title: \"Navigate to the Latch Data tab on the left panel.\",\n children: [_jsx(_components.p, {\n children: \"Use the ‘Upload’ modal found on the top right, and upload your raw .fastq or .fastq.gz files to Latch Data with the upload modal.\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna1.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })]\n })\n }), \"\\n\", _jsx(Heading, {\n level: \"3\",\n id: \"set-up-samplesheet-on-latch-registry\",\n children: \"Set up samplesheet on Latch Registry\"\n }), \"\\n\", _jsxs(Steps, {\n children: [_jsxs(Step, {\n title: \"Navigate to the Latch Registry tab on the left panel.\",\n children: [_jsx(_components.p, {\n children: \"Create new Project (if needed) and a new Sheet under that Project for the experiment being run.\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna2.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })]\n }), _jsx(Step, {\n title: \"Select the ‘Import -\u003e Bulk Import Sequencing Data’ modal on the top right of the screen.\",\n children: _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna3.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })\n }), _jsx(Step, {\n title: \"Choose the folder containing your raw RNAseq data and click ‘Select’.\",\n children: _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna4.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })\n }), _jsx(Step, {\n title: \"Confirm or modify name parsing method used to auto-group your samples and click ‘Next’.\",\n children: _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna5.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })\n }), _jsx(Step, {\n title: \"Fill in ‘fastq_1’ and ‘fastq_2’ for your forward and reverse read file respectively and click ‘Import’.\",\n children: _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna6.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })\n }), _jsx(Step, {\n title: \"This will generate a samplesheet on Latch Registry for your data.\",\n children: _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna7.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })\n })]\n }), \"\\n\", _jsx(Heading, {\n level: \"3\",\n id: \"launch-nf-core-rnaseq-latch-workflow\",\n children: \"Launch ‘nf-core/rnaseq’ Latch Workflow\"\n }), \"\\n\", _jsxs(Steps, {\n children: [_jsxs(Step, {\n title: \"Navigate to the Latch Workflows tab on the left panel.\",\n children: [_jsx(_components.p, {\n children: \"Choose the ‘nf-core/rnaseq’ workflow in ‘All Workflows’ or My Workflows’ (if you have added it).\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna8.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })]\n }), _jsx(Step, {\n title: \"Import samplesheet with ‘Import Rows from Registry’.\",\n children: _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna9.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })\n }), _jsx(Step, {\n title: \"Choose needed samplesheet, followed by needed samples (select all on top left if needed.\",\n children: _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna10.png\"\n })\n })\n }), _jsxs(Step, {\n title: \"Map samplesheet columns to workflow parameters and click ‘Import’.\",\n children: [_jsx(Note, {\n children: \"Click on the (x) for strandedness in most cases - only use strandedness if you have an nf-core specific strandedness column in your metadata.\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna11.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })]\n }), _jsxs(Step, {\n title: \"Choose ‘Reference Genome’ from ‘Latch Verified Reference Genome’ tab.\",\n children: [_jsx(_components.p, {\n children: \"Or choose your own Reference FASTA and GTF in the ‘Custom Reference Genome’ tab.\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna12.png\",\n className: \"rounded-md\"\n })\n })]\n }), _jsx(Step, {\n title: \"[Optional - Advanced] Choose alignment method or pseudoalignment method.\",\n children: _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna13.png\",\n className: \"rounded-md\"\n })\n })\n }), _jsxs(Step, {\n title: \"[Fill in a ‘Run Name’ and hit ‘Launch Execution’.\",\n children: [_jsx(_components.p, {\n children: \"Do not use spaces in the Run Name.\"\n }), _jsx(Note, {\n children: \"We recommend leaving the Output Directory to its default location.\"\n }), _jsxs(_components.p, {\n children: [\"(Optional - Advanced) Choose other parameters in ‘Optional Arguments’.\\n\", _jsx(Note, {\n children: \"There are descriptions for every parameter available when you hover above the (i) symbol on a parameter name.\"\n })]\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna14.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })]\n }), _jsxs(Step, {\n title: \"[Optional] Monitor the execution under ‘All Executions’.\",\n children: [_jsx(_components.p, {\n children: \"Double click the execution to be taken to detailed logs.\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna15.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })]\n }), _jsxs(Step, {\n title: \"Once complete, the output will be found in the output directory under your provided run name.\",\n children: [_jsx(_components.p, {\n children: \"Useful outputs are the run HTML report and all the computational outputs in the folder that matches the name of the aligner you used.\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna16.png\",\n className: \"rounded-md\"\n })\n })]\n })]\n }), \"\\n\", _jsx(Heading, {\n level: \"2\",\n id: \"differential-gene-expression\",\n children: \"Differential Gene Expression\"\n }), \"\\n\", _jsx(Heading, {\n level: \"3\",\n id: \"launch-deseq2-differential-expression-latch-workflow\",\n children: \"Launch ‘DESeq2 (Differential Expression)’ Latch Workflow\"\n }), \"\\n\", _jsxs(Steps, {\n children: [_jsxs(Step, {\n title: \"Navigate to the Latch Workflows tab on the left panel.\",\n children: [_jsx(_components.p, {\n children: \"Choose the ‘DESeq2 (Differential Expression)’ workflow in ‘All Workflows’ or My Workflows’ (if you have added it).\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna17.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })]\n }), _jsxs(Step, {\n title: \"Choose your input counts file from the outputs of ‘nf-core/rnaseq’.\",\n children: [_jsx(Note, {\n children: \"All outputs from ‘nf-core/rnaseq’ have an output folder called ‘deseq2_counts’ with a TSV file that is the optimal input for DESeq2.\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna18.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna19.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })]\n }), _jsxs(Step, {\n title: \"Choose your conditions for your samples in the ‘Manual Input’ design matrix tab.\",\n children: [_jsx(_components.p, {\n children: \"Or choose advanced conditions for your samples in the ‘File/Registry’ tab through Latch Data or Latch Registry.\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna20.png\",\n className: \"rounded-md\"\n })\n })]\n }), _jsxs(Step, {\n title: \"Choose ‘Report Name’ and hit ‘Launch Workflow’.\",\n children: [_jsx(Note, {\n children: \"We recommend leaving the Output to its default location.\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna21.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })]\n })]\n }), \"\\n\", _jsx(Heading, {\n level: \"3\",\n id: \"visualize-differential-gene-expression-outputs-in-latch-plots\",\n children: \"Visualize differential gene expression outputs in Latch Plots\"\n }), \"\\n\", _jsxs(Steps, {\n children: [_jsxs(Step, {\n title: \"Navigate to the Latch Plots tab on the left panel.\",\n children: [_jsx(_components.p, {\n children: \"Choose the ‘Differential Gene Expression Visualizer (0.0.6)’ template.\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna22.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })]\n }), _jsx(Step, {\n title: \"Once the DESeq2 run is done, choose your outputted run (or select from Latch Data if a custom output location was used) and scroll through for QC graphs and heatmaps.\",\n children: _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna23.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })\n }), _jsx(Step, {\n title: \"Choose ‘Contrast Conditions’ and ‘Genes of Interest’ for comparison and visualize Volcano and MA Plots.\",\n children: _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna24.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })\n }), _jsxs(Step, {\n title: \"If needed, turn on ‘Dev Mode’ in the top right and add more plots or code blocks \u003cRedirect to Plots Wiki\u003e.\",\n children: [_jsx(Note, {\n children: \"Click on the (x) for strandedness in most cases - only use strandedness if you have an nf-core specific strandedness column in your metadata.\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna25.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })]\n })]\n }), \"\\n\", _jsx(Heading, {\n level: \"2\",\n id: \"pathway-enrichment\",\n children: \"Pathway Enrichment\"\n }), \"\\n\", _jsx(Heading, {\n level: \"3\",\n id: \"launch-pathway-enrichment-analysis-latch-workflow\",\n children: \"Launch ‘Pathway Enrichment Analysis’ Latch Workflow\"\n }), \"\\n\", _jsxs(Steps, {\n children: [_jsxs(Step, {\n title: \"Navigate to the Latch Workflows tab on the left panel.\",\n children: [_jsx(_components.p, {\n children: \"Choose the ‘Pathway Enrichment Analysis’ workflow in ‘All Workflows’ or My Workflows’ (if you have added it).\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna26.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })]\n }), _jsxs(Step, {\n title: \"Choose your needed contrast file from the DESeq2 run output.\",\n children: [_jsx(_components.p, {\n children: \"Each run will have a ‘Data/Contrast’ folder with a file for every comparison created in DESeq2.\"\n }), _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna27.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })]\n }), _jsx(Step, {\n title: \"Choose your ‘Species’ and ‘Run Name’ and hit ‘Launch Workflow’.\",\n children: _jsx(ZoomImage, {\n children: _jsx(\"img\", {\n src: \"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/images/bulk-rna-seq-quant/bulkrna28.png\",\n className: \"w-full border-slate-100 border rounded-md\"\n })\n })\n }), _jsx(Step, {\n title: \"\\tUseful outputs are the final ‘Report.html’ generated.\",\n children: _jsx(\"iframe\", {\n width: \"560\",\n height: \"315\",\n src: \"https://www.youtube.com/embed/-z7Zb06EM_Y\",\n frameborder: \"0\",\n allow: \"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture\",\n allowfullscreen: true\n })\n })]\n }), \"\\n\", _jsx(\"br\", {}), \"\\n\", _jsx(\"br\", {}), \"\\n\", _jsx(Card, {\n title: \"Bulk RNA-seq Overview\",\n href: \"/workflows/bulk-rna-seq-deep-dive\",\n icon: _jsx(_components.svg, {\n width: \"24\",\n height: \"24\",\n viewBox: \"0 0 24 24\",\n fill: \"none\",\n xmlns: 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children: \"For a detailed overview of how Bulk-RNA Seq works, read our article.\"\n })\n })]\n });\n}\nfunction MDXContent(props = {}) {\n const {wrapper: MDXLayout} = Object.assign({}, _provideComponents(), props.components);\n return MDXLayout ? _jsx(MDXLayout, Object.assign({}, props, {\n children: _jsx(_createMdxContent, props)\n })) : _createMdxContent(props);\n}\nreturn {\n default: MDXContent\n};\nfunction _missingMdxReference(id, component) {\n throw new Error(\"Expected \" + (component ? \"component\" : \"object\") + \" `\" + id + \"` to be defined: you likely forgot to import, pass, or provide it.\");\n}\n","frontmatter":{},"scope":{"mintConfig":{"$schema":"https://mintlify.com/schema.json","name":"LatchBio","logo":{"light":"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/logo/light.svg","dark":"https://mintlify.s3-us-west-1.amazonaws.com/latchbio/logo/dark.svg"},"favicon":"/favicon.png","colors":{"primary":"#001AAE","light":"#92A2FF","dark":"#92A2FF"},"topbarCtaButton":{"name":"Sign Up","url":"https://console.latch.bio/signup"},"topbarLinks":[{"url":"mailto:support@latch.bio","name":"Contact Us","_id":"672464fb85507cebe4ae6679"},{"url":"https://console.latch.bio/","name":"Log 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