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Biostar HI-C
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</div> </div> </div> </div> <div class="post open item" data-value="9598433"> <div class="stats"> <div class="ui mini stat left label"> <div>2</div> <div>votes</div> </div> <div class="ui label stat mini news open bookmark"> <div>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>541</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> News: <a href="/p/9598433/"> Course on Manuel Genome Curation using PretextView (Online) </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/HI-C/"> HI-C </a> <a class="ptag" href="/tag/Genome-Assembly/"> Genome-Assembly </a> <a class="ptag" href="/tag/Manuel-Curation/"> Manuel-Curation </a> <a class="ptag" href="/tag/PretextView/"> PretextView </a> </div> <div class="right floated muted"> updated 4 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/19658/"> <span itemprop="name">shinken123</span> </a> ▴ 150 • written 9 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/32251/"> <span itemprop="name">Physalia-courses</span> </a> ★ 2.6k </div> </div> </div> </div> <div class="post open item" data-value="9603712"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini news open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>243</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> News: <a href="/p/9603712/"> Eukaryotic Genome Assembly Using PacBio and Hi-C course (4-8 November) </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/Genome-Assembly/"> Genome-Assembly </a> <a class="ptag" href="/tag/PacBio/"> PacBio </a> <a class="ptag" href="/tag/Long-reads/"> Long-reads </a> <a class="ptag" href="/tag/Hi-C/"> Hi-C </a> </div> <div class="right floated muted"> <span> 6 months ago by <a href="/u/32251/"> Physalia-courses </a> ★ 2.6k </span> </div> </div> </div> </div> <div class="post open item" data-value="9602838"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini question open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>238</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9602838/"> Hi-C Data and RNA-seq in a Non-Cell-Specific Context (Human Blood) </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/RNAexpression/"> RNAexpression </a> <a class="ptag" href="/tag/interactions/"> interactions </a> <a class="ptag" href="/tag/repeats/"> repeats </a> <a class="ptag" href="/tag/Hi-C/"> Hi-C </a> </div> <div class="right floated muted"> <span> 6 months ago by <a href="/u/137123/"> Smriti </a> ▴ 40 </span> </div> </div> </div> </div> <div class="post open item" data-value="9594408"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>2</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>965</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9594408/"> Why does my Hi-C contact map show large regions making little to no contact? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/BWA-MEM2/"> BWA-MEM2 </a> <a class="ptag" href="/tag/Hi-C/"> Hi-C </a> <a class="ptag" href="/tag/PretextMap/"> PretextMap </a> </div> <div class="right floated muted"> <span> 8 months ago by <a href="/u/144545/"> Winter </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" 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<div class="stats"> <div class="ui mini stat left label"> <div>2</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers accepted answer bookmark"> <div>2</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>828</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9593719/"> Can I merge Hi-C fastq files from different lanes? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/GenomeAssembly/"> GenomeAssembly </a> <a class="ptag" href="/tag/BWA-MEM2/"> BWA-MEM2 </a> <a class="ptag" href="/tag/Hi-C/"> Hi-C </a> </div> <div class="right floated muted"> updated 11 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/18713/"> <span itemprop="name">GenoMax</span> </a> <i class="ui muted bolt icon"></i> 150k • written 11 months ago by <a itemprop="author" itemscope 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href="/tag/assembly/"> assembly </a> <a class="ptag" href="/tag/genome/"> genome </a> <a class="ptag" href="/tag/Hi-C/"> Hi-C </a> </div> <div class="right floated muted"> <span> 13 months ago by <a href="/u/41599/"> rj.rezwan </a> ▴ 10 </span> </div> </div> </div> </div> <div class="post open item" data-value="9586557"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>8</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>1.3k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9586557/"> Can somebody guide me to setting up FAN-C module for hic analysis in my ubuntu ? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/fanc/"> fanc </a> <a class="ptag" href="/tag/HI-C/"> HI-C </a> <a class="ptag" href="/tag/hic/"> hic </a> <a 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spaced"> <a href="/p/9611102/"> Answer: Annotate GFA with coverage depth</a> by <a href="/u/58401/">Jordan M Eizenga </a> <span> ▴ 690 </span> <div class="muted"> You can annotate Bandage visualizations using a CSV with a certain structure, so you can process the `vg depth` TSV into Bandage's expected… </div> </div> <div class="item spaced"> <a href="/p/9611101/"> Answer: Query coverage high, E-value low, and identity low - Blastp results interpretati</a> by <a href="/u/56237/">Mensur Dlakic </a> <span> ★ 29k </span> <div class="muted"> Either you are not clear what homologous sequences mean, or you are using some internal definition that makes sense to you. Let's pick an `… </div> </div> <div class="item spaced"> <a href="/p/9611099/"> Answer: Methods for directional pathway analysis of DEGs?</a> by <a href="/u/13578/">Gordon Smyth </a> <span> ★ 7.9k </span> <div class="muted"> limma provides a suite of directional pathway analysis functions that are integrated with its DE procedures. They are based on competitive … </div> </div> <div class="item spaced"> <a href="/p/9611097/"> Comment: Discrepancy between positions on IGV and NCBI's PrimerBLAST</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> > It showed me the same positions as that of PrimerBLAST. So we know that result is correct. You made the BED file manually? It is in cor… </div> </div> <div class="item spaced"> <a href="/p/9611096/"> Comment: MultiQC_report</a> by <a href="/u/14100/">Phil Ewels </a> <span> ★ 1.4k </span> <div class="muted"> Thanks for spotting! As mentioned below, it's samples * top adapters. I've made an issue here: https://github.com/MultiQC/MultiQC/issues/31… </div> </div> <div class="item spaced"> <a href="/p/9611095/"> Comment: MultiQC_report</a> by <a href="/u/14100/">Phil Ewels </a> <span> ★ 1.4k </span> <div class="muted"> This is exactly the case. Surprising that no-one else has brought this up in 10 years! I've created an issue here to fix it: https://gith… </div> </div> <div class="item spaced"> <a href="/p/9611094/"> Comment: Poor alignment rates using Bowtie</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> Quick representative check with a random Illumina dataset (50 bp, 200K reads from it). Bowtie v.1.3.1 and `mature.fa` downloaded from miR… </div> </div> <div class="item spaced"> <a href="/p/9611093/"> Comment: Why does Radian run so much slower than vanilla R?</a> by <a href="/u/2/">Istvan Albert </a> <span> <i class="ui muted bolt icon"></i> 102k </span> <div class="muted"> I would recommend asking this on the radian GitHub discussion page. </div> </div> <div class="item spaced"> <a href="/p/9611090/"> Comment: Poor alignment rates using Bowtie</a> by <a href="/u/2/">Istvan Albert </a> <span> <i class="ui muted bolt icon"></i> 102k </span> <div class="muted"> That being said, I'd like to hear whether the Us in the reference made any difference. It is conceivable that Bowtie 1 treats U as a T. L… </div> </div> <div class="item spaced"> <a href="/p/9611089/"> Comment: C.reinhardtii single-cell Seurat object - gene names instead of loci</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> > BD Rhapsody protocols That is important to know. Perhaps the issue is with the way you converted the GFF3 to GTF. What software did you … </div> </div> <div class="item spaced"> <a href="/p/9611085/"> Comment: C.reinhardtii single-cell Seurat object - gene names instead of loci</a> by <a href="/u/149753/">Ana </a> <span> • 0 </span> <div class="muted"> Thank you for your answer! Unfortunalety, NCBI doesn't have the latest version of the genome and annotations for this organism (v6.1), so I… </div> </div> <div class="item spaced"> <a href="/p/9611084/"> Comment: Has anybody worked with C.reinhardtii single-cell before and could help me get t</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> It is always safer to get sequence/annotations from standard sources like NCBI/Ensembl so no manipulations are required to make the data wo… </div> </div> <div class="item spaced"> <a href="/p/9611083/"> Comment: Snakemake Global Environment Container</a> by <a href="/u/71816/">DBScan </a> <span> ▴ 470 </span> <div class="muted"> How are you running snakemake? </div> </div> <div class="item spaced"> <a href="/p/9611081/"> Comment: Poor alignment rates using Bowtie</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> Looking at the size distribution the data must already be pre-trimmed so it does not make sense to trim again. You should merge data from t… </div> </div> <div class="item spaced"> <a href="/p/9611079/"> Answer: MultiQC_report</a> by <a href="/u/87334/">Basti </a> <span> ★ 2.0k </span> <div class="muted"> I think it just counts the total number of lines while there could be multiple adapters types per sample (ex : illumina_universal_adapter, … </div> </div> </div> </div> </div> </div> </div> </div> <div id="traffic">Traffic: 1777 users visited in the last hour</div> </div> <div class="ui three center aligned column stackable tiny grid"> <div class=" left aligned column" style="padding-right: 13%"> <b>Content</b> <a href="/#search-anchor">Search</a><br> <a href="/user/list/">Users</a><br> <a href="/t/">Tags</a><br> <a href="/b/list/">Badges</a> </div> <div class="left aligned column" style="padding-right: 12%"> <b>Help</b> <a href="/info/about/">About</a><br> <a href="/info/faq/">FAQ</a><br> </div> <div class=" left aligned column"> <b>Access</b> <a href="/info/rss/">RSS</a><br> <a href="/info/api/">API</a><br> <a href="#">Stats</a> </div> </div> <div class="ui divider"></div> <div class="ui vertical center aligned basic segment"> <p>Use of this site constitutes acceptance of our <a href="/info/policy/">User Agreement and Privacy Policy</a>.</p> <div class="smaller muted"> Powered by the <a href="https://github.com/ialbert/biostar-central" class="ui image"> <img src="/static/images/badge-forum.svg"></a> version 2.3.6 </div> </div> <div align="center"> <script type="text/javascript" src="//rf.revolvermaps.com/0/0/0.js?i=5j83en1rmbf&d=2&p=2&b=0&w=293&g=2&f=arial&fs=12&r=0&c0=362b05&c1=375363&c2=000000&ic0=0&ic1=0" async="async"></script> </div> <div align="center" style="margin-top:1ex"> <script type="text/javascript" src="//rh.revolvermaps.com/0/0/6.js?i=7pci0h9z8v6&m=0&s=300&c=ff0000&cr1=ffffff&f=arial& amp;l=0" async="async"></script> </div> </div> </body> </html>