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</a> <i class="ui muted bolt icon"></i> 11k • written 11 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/42089/"> <span itemprop="name">Sophia</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610963"> <div class="stats"> <div class="ui mini stat left label"> <div>3</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>4</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>163</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610963/"> Extract length of sample sequence from vcf </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/microsatellites/"> microsatellites </a> <a class="ptag" href="/tag/bcftools/"> bcftools </a> <a class="ptag" href="/tag/vcf/"> vcf </a> <a class="ptag" href="/tag/indels/"> indels </a> <a class="ptag" href="/tag/variants/"> variants </a> </div> <div class="right floated muted"> updated 3 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/49414/"> <span itemprop="name">Billy Rowell</span> </a> ▴ 500 • written 10 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/143034/"> <span itemprop="name">jahnreinhard.ringger</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610970"> <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>41</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610970/"> How to obtain TPM data after batch effect correction from count data obtained using RSEM </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/STAR/"> STAR </a> <a class="ptag" href="/tag/RNA-seq/"> RNA-seq </a> <a class="ptag" href="/tag/Batch/"> Batch </a> <a class="ptag" href="/tag/RSEM/"> RSEM </a> <a class="ptag" href="/tag/effect/"> effect </a> </div> <div class="right floated muted"> <span> 7 hours ago by <a href="/u/10896/"> Apprentice </a> ▴ 170 </span> </div> </div> </div> </div> <div class="post open item" data-value="225812"> <div class="stats"> <div class="ui mini stat left label"> <div>835</div> <div>votes</div> </div> <div class="ui label stat mini news has_answers open bookmark"> <div>169</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>172k</div> <div>views</div> </div> <div class="subs">110 follow</div> </div> <div class="content"> <div class="title mini header"> News: <a href="/p/225812/"> The Biostar Handbook. 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<div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610942/"> MultiQC_report </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/content_multiqc_fastqc/"> content_multiqc_fastqc </a> <a class="ptag" href="/tag/Quality_control_/"> Quality_control_ </a> <a class="ptag" href="/tag/Adapter/"> Adapter </a> </div> <div class="right floated muted"> updated 3 hours 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 13 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149438/"> <span itemprop="name">AIMAR</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610950"> <div class="stats"> <div class="ui mini stat left label"> <div>2</div> <div>votes</div> </div> <div class="ui label stat mini forum open bookmark"> <div>2</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>134</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Forum: <a href="/p/9610950/"> How to get into research for an absolute beginners </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/research/"> research </a> </div> <div class="right floated muted"> updated 9 hours 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 13 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149796/"> <span itemprop="name">jpeduprep</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610947"> <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>55</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> News: <a href="/p/9610947/"> Online course — Comparative Genomics — 7–11 April </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/SNVs/"> SNVs </a> <a class="ptag" href="/tag/ComparativeGenomics/"> ComparativeGenomics </a> <a class="ptag" href="/tag/SVs/"> SVs </a> <a class="ptag" href="/tag/GenomeAnnotation/"> GenomeAnnotation </a> </div> <div class="right floated muted"> <span> 13 hours ago by <a href="/u/32251/"> Physalia-courses </a> ★ 2.6k </span> </div> </div> </div> </div> <div class="post open item" data-value="9610940"> <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>2</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>112</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610940/"> how to do a corellation analysis of multiple CRISPR data sets </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/batch-effect./"> batch-effect. </a> <a class="ptag" href="/tag/crispr/"> crispr </a> <a class="ptag" href="/tag/screen/"> screen </a> <a class="ptag" href="/tag/correlation/"> correlation </a> </div> <div class="right floated muted"> <span> 9 hours ago by <a href="/u/2295/"> Assa Yeroslaviz </a> ★ 1.9k </span> </div> </div> </div> </div> <div class="post open item" data-value="9610832"> <div class="stats"> <div class="ui mini stat left label"> <div>8</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>4</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>339</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610832/"> Alternatives to UCSC genome browser for obtaining gene coordinates </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/browser/"> browser </a> <a class="ptag" href="/tag/ucsc/"> ucsc </a> </div> <div class="right floated muted"> updated 10 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/13619/"> <span itemprop="name">LauferVA</span> </a> <i class="ui muted bolt icon"></i> 4.6k • written 3 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/14084/"> <span itemprop="name">shpak.max</span> </a> ▴ 60 </div> </div> </div> </div> <div class="post open item" data-value="9610925"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</div> </div> <div class="ui label stat mini tool has_answers open bookmark"> <div>9</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>312</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Tool: <a href="/p/9610925/"> Introducing Grantease: Go From RFA to First Draft Grant Proposal in 15 Minutes </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/ai/"> ai </a> <a class="ptag" href="/tag/biology/"> biology </a> <a class="ptag" href="/tag/grants/"> grants </a> <a class="ptag" href="/tag/nih/"> nih </a> <a class="ptag" href="/tag/litreview/"> litreview </a> </div> <div class="right floated muted"> updated 4 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/40195/"> <span itemprop="name">jared.andrews07</span> </a> ★ 18k • written 1 day ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149787/"> <span itemprop="name">Will</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610931"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini job open bookmark"> <div>0</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>90</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Job: <a href="/p/9610931/"> Postdoctoral Position in Computational Protein Design and Molecular Modelling </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/opportunity/"> opportunity </a> <a class="ptag" href="/tag/postdoc/"> postdoc </a> </div> <div class="right floated muted"> <span> 1 day ago by <a href="/u/149789/"> Sophie </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="9610923"> <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>3</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>167</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610923/"> Modify read groups in BAM file </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/samtools/"> samtools </a> <a class="ptag" href="/tag/BAM/"> BAM </a> <a class="ptag" href="/tag/picard/"> picard </a> <a class="ptag" href="/tag/DRAGEN/"> DRAGEN </a> </div> <div class="right floated muted"> updated 3 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/30615/"> <span itemprop="name">1769mkc</span> </a> ★ 1.2k • written 1 day ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149784/"> <span itemprop="name">Alex</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610921"> <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>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>133</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610921/"> How to put distinct colors to connection bridges in the Sankey plot ? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/R/"> R </a> <a class="ptag" href="/tag/Python/"> Python </a> <a class="ptag" href="/tag/Sankey/"> Sankey </a> </div> <div class="right floated muted"> updated 15 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/3919/"> <span itemprop="name">zx8754</span> </a> <i class="ui muted bolt icon"></i> 12k • written 1 day ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/115665/"> <span itemprop="name">ohtang7</span> </a> ▴ 40 </div> </div> 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<div>0</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>9</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>368</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610866/"> Find the reads which correspond to DP of vcf </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/bam/"> bam </a> <a class="ptag" href="/tag/variant/"> variant </a> <a class="ptag" href="/tag/vcf/"> vcf </a> <a class="ptag" href="/tag/sam2tsv/"> sam2tsv </a> </div> <div class="right floated muted"> updated 1 day ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/30/"> <span itemprop="name">Pierre Lindenbaum</span> </a> <i class="ui muted bolt icon"></i> 165k • written 2 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/52236/"> <span 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<div class="item spaced"> <a href="/p/9610979/"> Comment: Modify read groups in BAM file</a> by <a href="/u/30615/">1769mkc </a> <span> ★ 1.2k </span> <div class="muted"> is this onboard or basespace or ICA? dragen </div> </div> <div class="item spaced"> <a href="/p/9610978/"> Comment: MultiQC_report</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> That is pretty odd. Like you were advised above you could try to open an issue with the devs. I don't think I have ever seen this problem. … </div> </div> <div class="item spaced"> <a href="/p/9610977/"> Answer: Facing issue with output of nextflow pipeline</a> by <a href="/u/148661/">mmhryc </a> <span> • 0 </span> <div class="muted"> With nextflow you don't want to manage paths manually. Instead of creating a hardcoded path you should let it output the results into whate… </div> </div> <div class="item spaced"> <a href="/p/9610976/"> Answer: Choosing the best clustering method for a certain methylation data</a> by <a href="/u/9490/">5heikki </a> <span> <i class="ui muted bolt icon"></i> 11k </span> <div class="muted"> [Affinity propagation][1] is the answer to all my clustering needs [1]: https://utstat.toronto.edu/reid/sta414/frey-affinity.pdf </div> </div> <div class="item spaced"> <a href="/p/9610975/"> Comment: Modify read groups in BAM file</a> by <a href="/u/149784/">Alex </a> <span> • 0 </span> <div class="muted"> Thanks Istvan, this seems like a reasonable enough solution that could be scripted across large batches of files. I'll give it a shot. Was … </div> </div> <div class="item spaced"> <a href="/p/9610974/"> Comment: MultiQC_report</a> by <a href="/u/149438/">AIMAR </a> <span> • 0 </span> <div class="muted"> No I don't, when I said errors I mean it shows 267 samples for the adapter content while I just have 50 samples of paired-end read = 100 re… </div> </div> <div class="item spaced"> <a href="/p/9610973/"> Comment: MultiQC_report</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> > in this report multiqc missed 3 samples (6 reports ) and still made the error with the adapter content. Do you have any oddities in samp… </div> </div> <div class="item spaced"> <a href="/p/9610972/"> Answer: Extract length of sample sequence from vcf</a> by <a href="/u/49414/">Billy Rowell </a> <span> ▴ 500 </span> <div class="muted"> This is hacky and definitely not prod ready, but if the goal is to get the length and not the sequence, you could use bcftools/paste/bc to … </div> </div> <div class="item spaced"> <a href="/p/9610971/"> Comment: Extract length of sample sequence from vcf</a> by <a href="/u/13619/">LauferVA </a> <span> <i class="ui muted bolt icon"></i> 4.7k </span> <div class="muted"> you probably want to be working wihta bam file for this .. </div> </div> <div class="item spaced"> <a href="/p/9610969/"> Comment: MultiQC_report</a> by <a href="/u/149438/">AIMAR </a> <span> • 0 </span> <div class="muted"> ![enter image description here][1] Here is the screenshot, in this report multiqc missed 3 samples (6 reports ) and still made the error… </div> </div> <div class="item spaced"> <a href="/p/9610968/"> Comment: Extract length of sample sequence from vcf</a> by <a href="/u/2/">Istvan Albert </a> <span> <i class="ui muted bolt icon"></i> 102k </span> <div class="muted"> Once you slice the reference genome, the positions in the VCF won't match the reference. For your method to work you would need to shift th… </div> </div> <div class="item spaced"> <a href="/p/9610967/"> Comment: Introducing Grantease: Go From RFA to First Draft Grant Proposal in 15 Minutes</a> by <a href="/u/40195/">jared.andrews07 </a> <span> ★ 18k </span> <div class="muted"> The source is this tool's literature review feature with the prompt "Impacts of AI on human creativity". The references contain some charac… </div> </div> <div class="item spaced"> <a href="/p/9610966/"> Comment: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand</a> by <a href="/u/d3504e25/">Paulo </a> <span> ▴ 10 </span> <div class="muted"> Thanks for the feedback, Istvan! Taking that into account, I made a few small tweaks and rewrote the script as follows: (I'm sharing it ju… </div> </div> <div class="item spaced"> <a href="/p/9610965/"> Comment: how to do a corellation analysis of multiple CRISPR data sets</a> by <a href="/u/2295/">Assa Yeroslaviz </a> <span> ★ 1.9k </span> <div class="muted"> I just modified my response. sorry for the missing information </div> </div> </div> </div> </div> </div> </div> </div> <div id="traffic">Traffic: 1691 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>