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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>359</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 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/30615/"> <span itemprop="name">1769mkc</span> </a> ★ 1.2k • written 4 days 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="9610866"> <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>9</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>561</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 4 days 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 5 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/52236/"> <span itemprop="name">totoroGirl</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610368"> <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>3</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>331</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610368/"> Higher number of reads mapped to transcriptome vs genome in star mapping </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/riboseq/"> riboseq </a> <a class="ptag" href="/tag/star/"> star </a> <a class="ptag" href="/tag/bam/"> bam </a> <a class="ptag" href="/tag/transcriptome/"> transcriptome </a> <a class="ptag" href="/tag/alignment/"> alignment </a> </div> <div class="right floated muted"> updated 18 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/16790/"> <span itemprop="name">i.sudbery</span> </a> <i class="ui muted bolt icon"></i> 21k • written 18 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149601/"> <span itemprop="name">paguirreazorin</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610164"> <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>2</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>386</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610164/"> Parsing BAM file per cell from Smart-Seq2 dataset </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/starsolo/"> starsolo </a> <a class="ptag" href="/tag/star/"> star </a> <a class="ptag" href="/tag/BAM/"> BAM </a> <a class="ptag" href="/tag/smartseq2/"> smartseq2 </a> <a class="ptag" href="/tag/alignment/"> alignment </a> </div> <div class="right floated muted"> updated 23 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/30020/"> <span itemprop="name">dsull</span> </a> ★ 7.3k • written 24 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/124294/"> <span itemprop="name">brutonk</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9609324"> <div class="stats"> <div class="ui mini stat left label"> <div>2</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>281</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9609324/"> An alternative to haplotype phasing - assembly? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/samtools/"> samtools </a> <a class="ptag" href="/tag/assembly/"> assembly </a> <a class="ptag" href="/tag/BAM/"> BAM </a> <a class="ptag" href="/tag/spades/"> spades </a> <a class="ptag" href="/tag/phasing/"> phasing </a> </div> <div class="right floated muted"> <span> 6 weeks ago by <a href="/u/51011/"> Jess </a> ▴ 60 </span> </div> </div> </div> </div> <div class="post open item" data-value="9608965"> <div class="stats"> <div class="ui mini stat left label"> <div>6</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers accepted answer bookmark"> <div>5</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>509</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9608965/"> ATAC-seq paired-end data peakcalling on MACS3 - BAMPE vs (BAM and shift with extsize) </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/MACS3/"> MACS3 </a> <a class="ptag" href="/tag/BAMPE/"> BAMPE </a> <a class="ptag" href="/tag/BAM/"> BAM </a> <a class="ptag" href="/tag/Peakcalling/"> Peakcalling </a> <a class="ptag" href="/tag/ATAC-seq/"> ATAC-seq </a> </div> <div class="right floated muted"> updated 7 weeks ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/25721/"> <span itemprop="name">ATpoint</span> </a> <i class="ui muted bolt icon"></i> 87k • written 7 weeks ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/135797/"> <span itemprop="name">Manko47</span> </a> ▴ 10 </div> </div> </div> </div> <div class="post open item" data-value="9608666"> <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>17</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>1.2k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9608666/"> Unable to get to BAM file from SAM using samtools </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/SAM/"> SAM </a> </div> <div class="right floated muted"> <span> 7 weeks ago by <a href="/u/144005/"> alejandro.mejiam1 </a> ▴ 20 </span> </div> </div> </div> </div> <div class="post open item" data-value="9608233"> <div class="stats"> <div class="ui mini stat left label"> <div>2</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>304</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9608233/"> Origin of unmapped reads </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/scrna/"> scrna </a> <a class="ptag" href="/tag/bam/"> bam </a> <a class="ptag" href="/tag/mapping/"> mapping </a> <a class="ptag" href="/tag/sequencing/"> sequencing </a> <a class="ptag" href="/tag/shortreads/"> shortreads </a> </div> <div class="right floated muted"> updated 10 weeks ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/44316/"> <span itemprop="name">dthorbur</span> </a> ★ 2.9k • written 10 weeks ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/142138/"> <span itemprop="name">Kay</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9608147"> <div class="stats"> <div class="ui mini stat left label"> <div>14</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers accepted answer bookmark"> <div>12</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>1.1k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9608147/"> What additional info is found in BAM files from PacBio HiFi compared to Fastq files </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/bam/"> bam </a> <a class="ptag" href="/tag/hifi/"> hifi </a> <a class="ptag" href="/tag/fastq/"> fastq </a> <a class="ptag" href="/tag/pacbio/"> pacbio </a> </div> <div class="right floated muted"> updated 10 weeks ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/49414/"> <span itemprop="name">Billy Rowell</span> </a> ▴ 510 • written 10 weeks ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/216/"> <span itemprop="name">Eric Normandeau</span> </a> <i class="ui muted bolt icon"></i> 11k </div> </div> </div> </div> <div class="post open item" data-value="9608136"> <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>369</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9608136/"> capmq and verifybamid </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/bam/"> bam </a> <a class="ptag" href="/tag/capmq/"> capmq </a> <a class="ptag" href="/tag/vcf/"> vcf </a> <a class="ptag" href="/tag/verifyBAMID/"> verifyBAMID </a> </div> <div class="right floated muted"> <span> 10 weeks ago by <a href="/u/31132/"> Peter Chung </a> ▴ 210 </span> </div> </div> </div> </div> <div class="post open item" data-value="9608130"> <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>227</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9608130/"> Converting gaf files to sam/bam? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/bam/"> bam </a> <a class="ptag" href="/tag/gaf/"> gaf </a> <a class="ptag" href="/tag/sam/"> sam </a> </div> <div class="right floated muted"> <span> 6 weeks ago by <a href="/u/132180/"> guntul </a> ▴ 40 </span> </div> </div> </div> </div> <div class="post open item" data-value="9607944"> <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>261</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9607944/"> Plugging output files from phyluce phasing workflow into Structure </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/phyluce/"> phyluce </a> <a class="ptag" href="/tag/uce/"> uce </a> <a class="ptag" href="/tag/bam/"> bam </a> <a class="ptag" href="/tag/phasing/"> phasing </a> <a class="ptag" href="/tag/structure/"> structure </a> </div> <div class="right floated muted"> <span> 11 weeks ago by <a href="/u/148617/"> gabe.somarriba </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="9607943"> <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>263</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9607943/"> gcpp ERROR: [pbbam] read group ERROR: basecaller version is too short: </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/header/"> header </a> <a class="ptag" href="/tag/pacbio/"> pacbio </a> <a class="ptag" href="/tag/bam/"> bam </a> <a class="ptag" href="/tag/basecaller/"> basecaller </a> <a class="ptag" href="/tag/gcpp/"> gcpp </a> </div> <div class="right floated muted"> <span> 11 weeks ago by <a href="/u/148620/"> therosng </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="9607644"> <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 open bookmark"> <div>7</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>1.0k</div> <div>views</div> </div> <div class="subs">6 follow</div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9607644/"> Parsing error in sam file when converting to bam </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/samtools/"> samtools </a> <a class="ptag" href="/tag/bwa/"> bwa </a> <a class="ptag" href="/tag/fastq/"> fastq </a> <a class="ptag" href="/tag/bam/"> bam </a> <a class="ptag" href="/tag/sam/"> sam </a> </div> <div class="right floated muted"> updated 11 weeks 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 12 weeks ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/148522/"> <span itemprop="name">emily.coger</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9607757"> <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 accepted answer bookmark"> <div>1</div> <div>reply</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"> <a href="/p/9607757/"> samtools tview special character </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/rna/"> rna </a> </div> <div class="right floated muted"> updated 11 weeks 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 12 weeks ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/16198/"> <span itemprop="name">from the mountains</span> </a> ▴ 250 </div> </div> </div> </div> <div class="post open item" data-value="9607747"> <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>3</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>512</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9607747/"> NA12878, NA12891 and NA12892 gold standard samples information </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/standard/"> standard </a> <a class="ptag" href="/tag/gold/"> gold </a> <a class="ptag" href="/tag/variant/"> variant </a> <a class="ptag" href="/tag/BAM/"> BAM </a> <a class="ptag" href="/tag/calling/"> calling </a> </div> <div class="right floated muted"> updated 12 weeks ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/18713/"> <span 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href="/u/149848/">ngelbal </a> <span> • 0 </span> <div class="muted"> Can someone please provide me with a tool/sourcecode to convert a VCF into GEDMatch uploadable format? </div> </div> <div class="item spaced"> <a href="/p/9611047/"> Comment: Error in importing data from 10x genomics into RStudio</a> by <a href="/u/140322/">himanshu0102 </a> <span> • 0 </span> <div class="muted"> Yes, that is correct. </div> </div> <div class="item spaced"> <a href="/p/9611046/"> Comment: Polishing raw nanopore reads with Pacbio</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> Just a thought. You could make fake illumina reads from HiFi reads. </div> </div> <div class="item spaced"> <a href="/p/9611043/"> Comment: Error in importing data from 10x genomics into RStudio</a> by <a href="/u/30615/">1769mkc </a> <span> ★ 1.2k </span> <div class="muted"> to help you and at the same time other can help when you can cite what exactly you had ran the code, the Seurat version R session info etc,… </div> </div> <div class="item spaced"> <a href="/p/9611042/"> Answer: bbduk.sh trimming to BAM output file</a> by <a href="/u/14684/">Brian Bushnell </a> <span> <i class="ui muted bolt icon"></i> 20k </span> <div class="muted"> Hi Brent, at one time, and to some extent, BBDuk did trimming of sam/bam files. However, it's a very fiddly process because the cigar stri… </div> </div> <div class="item spaced"> <a href="/p/9611041/"> Answer: Identifying domain of long-read assembled contig</a> by <a href="/u/56237/">Mensur Dlakic </a> <span> ★ 29k </span> <div class="muted"> In my experience, [**tiara**](https://github.com/ibe-uw/tiara) works really well in classifying contigs between the 3 major kingdoms, plus … </div> </div> <div class="item spaced"> <a href="/p/9611040/"> Comment: I Built a Website That Summarizes Your Research with 5 Emojis</a> by <a href="/u/8494/">Ram </a> <span> <i class="ui muted bolt icon"></i> 45k </span> <div class="muted"> This post does not fit the theme of this forum. </div> </div> <div class="item spaced"> <a href="/p/9611039/"> Comment: Error in importing data from 10x genomics into RStudio</a> by <a href="/u/40195/">jared.andrews07 </a> <span> ★ 18k </span> <div class="muted"> Please learn [how to ask a good question](https://www.biostars.org/p/75548/). We are unable to help you given the information provided. </div> </div> <div class="item spaced"> <a href="/p/9611038/"> 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"> Super hard pass. This just enables the further flooding of study sections with low-quality, poorly thought-out drivel with a veneer of poli… </div> </div> <div class="item spaced"> <a href="/p/9611036/"> 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"> Can you check with the ` in silico` PCR tool at UCSC to see what that says : https://genome.ucsc.edu/cgi-bin/hgPcr PrimerBLAST is likely … </div> </div> <div class="item spaced"> <a href="/p/9611035/"> Comment: Introducing Grantease: Go From RFA to First Draft Grant Proposal in 15 Minutes</a> by <a href="/u/149787/">Will </a> <span> • 0 </span> <div class="muted"> Jared, I know you're highly skeptical. So, let's see if I can prove you wrong. Book a demo, and I'll walk you through the tool personally. </div> </div> <div class="item spaced"> <a href="/p/9611034/"> Comment: Identifying domain of long-read assembled contig</a> by <a href="/u/133258/">Gio </a> <span> • 0 </span> <div class="muted"> Has that been shown to be more precise that both? </div> </div> <div class="item spaced"> <a href="/p/9611033/"> Comment: About the Tool FASTP</a> by <a href="/u/149438/">AIMAR </a> <span> • 0 </span> <div class="muted"> Here's the command line I've used in my script to preprocess my data (DNA paired-end reads). By preprocess I mean adapter removal, trimming… </div> </div> <div class="item spaced"> <a href="/p/9611032/"> Comment: About the Tool FASTP</a> by <a href="/u/149438/">AIMAR </a> <span> • 0 </span> <div class="muted"> Understood, I think from now it's good cause I've checked the quality and it seems good than before. </div> </div> </div> </div> </div> </div> </div> </div> <div id="traffic">Traffic: 1847 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>