CINXE.COM
Biostar Open
<html> <head> <title> Biostar Open </title> <meta charset="UTF-8"> <meta name="viewport" content="width=device-width, initial-scale=1"> <link rel="icon" href="/static/forum_favicon.ico" type="image/x-icon"/> <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.2.1/jquery.min.js"></script> <!-- Global site tag (gtag.js) - Google Analytics --> <script async src="https://www.googletagmanager.com/gtag/js?id=UA-101522-12"></script> <script> window.dataLayer = window.dataLayer || []; function gtag() { dataLayer.push(arguments); } gtag('js', new Date()); gtag('config', "UA-101522-12"); </script> <link rel="stylesheet" href="/static/CACHE/css/output.07f6ec786af0.css" type="text/css"> <script src="/static/CACHE/js/output.10280c94381d.js"></script> </head> <body itemscope itemtype="https://schema.org/QAPage"> <div class="ui inverted container main"> <span class="menus"> <div class="ui borderless menu" id="topicbar"> <a class="item " href="/"> <i class="list icon"></i> Latest </a> <a class="item active " href="/t/open/"> <i class="envelope open icon"></i> Open </a> <a class="item " href="/t/jobs/"> <i class="briefcase icon"></i> Jobs </a> <a class="item " href="/t/tutorials/"> <i class="help circle icon"></i> Tutorials </a> <!-- <a class="item " href="/t/forum/"> <i class="file icon"></i> Forum </a> --> <a class="item " href="/t/"> <i class="tag icon"></i> Tags </a> <a class="item " href="/info/about/"> <i class="info circle icon"></i>About </a> <a class="item " href="/info/faq/"> <i class="info recycle icon"></i>FAQ </a> </div> <div class="ui labeled icon top attached evenly divided menu" id="menu-header" user-id="None"> <div class="header item" id="logo"> <a href="/"><img width="250px" src="/static/images/logo6.svg"></a> </div> <a class="item " href="/user/list/"> <i class="world icon"></i> Community </a> <a class="item " href="/planet/"> <i class="rss icon"></i> Planet </a> <a class="item " href="/new/post/"> <i class="edit icon"></i> New Post </a> <div class="right menu"> <a class="item " href="/accounts/login/" id="new-post"> <i class="sign-in icon"></i> Log In </a> </div> </div> </span> <span class="phone-menus"> <div class="header item" id="logo"> <a href="/"><img class="ui image" width="220px" src="/static/images/logo6.svg"></a> </div> <div class="ui labeled icon attached fluid pointing menu" id="menu-header"> <div class="ui left simple dropdown item"> <i class="bars icon"><i class="dropdown icon"></i></i> <div class="menu"> <a class="item " href="/new/post/"> <i class=" edit icon"></i>New Post </a> <a class="item " href="/"> <i class=" list icon"></i> Latest </a> <a class="item active " href="/t/open/"> <i class="envelope open icon"></i> Open </a> <a class="item " href="/t/news/"> <i class=" newspaper icon"></i> News </a> <a class="item " href="/t/jobs/"> <i class=" briefcase icon"></i> Jobs </a> <a class="item " href="/t/tutorials/"> <i class=" info circle icon"></i> Tutorials </a> <a class="item " href="/t/forum/"> <i class="file icon"></i> Forum </a> <a class="item " href="/t/"> <i class="tag icon"></i>Tags </a> <a class="item " href="/planet/"> <i class="rss icon"></i> Planet </a> <a class="item " href="/user/list/"> <i class=" world icon"></i> Users </a> </div> </div> <div class="ui right simple dropdown item"> </div> <div class="ui right simple dropdown item"> <i class="user icon"><i class="dropdown icon"></i></i> <div class="menu" id="login-opts"> <a class="item " href="/accounts/login/"><i class="sign-in icon"></i> Log In</a> <a class="item " href="/accounts/signup/"><i class="arrow circle up icon"></i> Sign Up</a> <a class="item "><i class="info circle icon"></i>About </a> </div> </div> </div> </span> <div class="ui bottom attached segment block"> <div class="ui stackable grid"> <div class="fit twelve wide content column"> <div class="ui basic segment search-bar" id="search-anchor"> <div class="center-text "> <form class="ui form" method="GET" action="/post/search/" style="margin: 0"> <div class="ui search"> <div class="ui icon input"> <input value="" class="search-input" type="text" name="query" placeholder="Search ... "> <i class="search icon"></i> </div> </div> </form> </div> </div> <div class="ui horizontal basic top-menu segments"> <div class="ui first segment"> <div class="ui small compact menu no-shadow"> <div class="ui simple dropdown item"> <i class="calendar plus icon"></i> <span class="tablet">Limit : all time</span> <i class="dropdown icon"></i> <div class="menu"> <a class="item" href="/t/open/?limit=all"> <i class="calendar plus icon"></i>all time </a> <a class="item" href="/t/open/?limit=today"> <i class="clock icon"></i>today </a> <a class="item" href="/t/open/?limit=week"> <i class="calendar minus outline icon"></i>this week </a> <a class="item" href="/t/open/?limit=month"> <i class="calendar alternate icon"></i>this month </a> <a class="item" href="/t/open/?limit=year"> <i class="calendar icon"></i>this year </a> </div> </div> </div> </div> <div class="ui page-bar segment"> <div class="ui small basic button no-shadow"> <i class="ui angle double left icon"> </i> </div> <span class="phone">1,000 results • Page </span> 1 of 20 <a class="ui small basic button no-shadow" href="/t/open/?page=2"> <i class="ui angle double right icon"></i> </a> </div> <div class="ui third segment"> <div class="ui small compact menu no-shadow float-right"> <div class="ui simple dropdown item"> <i class="list ol icon"></i> <span class="tablet">Sort: Rank</span> <i class="dropdown icon"></i> <div class="menu"> <a class="item" href="/t/open/?order=rank"> <i class="list ol icon"></i>Rank </a> <a class="item" href="/t/open/?order=views"> <i class="eye icon"></i>Views </a> <a class="item" href="/t/open/?order=votes"> <i class="thumbs up icon"></i>Votes </a> <a class="item" href="/t/open/?order=replies"> <i class="comments icon"></i>Replies </a> </div> </div> </div> </div> </div> <div class="ui divided items"> <div class="post open item" data-value="9611126"> <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>8</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611126/"> Using DEXseq on kallisto tsv outputs ? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/alignement/"> alignement </a> <a class="ptag" href="/tag/DEXseq/"> DEXseq </a> <a class="ptag" href="/tag/kallisto/"> kallisto </a> </div> <div class="right floated muted"> <span> 22 minutes ago by <a href="/u/143197/"> Gerard </a> ▴ 10 </span> </div> </div> </div> </div> <div class="post open item" data-value="9611116"> <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>32</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611116/"> GTDB-tk classify_wf </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/GTDB-tk/"> GTDB-tk </a> <a class="ptag" href="/tag/classification/"> classification </a> <a class="ptag" href="/tag/taxonomic/"> taxonomic </a> </div> <div class="right floated muted"> <span> 3 hours ago by <a href="/u/147797/"> pranjalarun10 </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="9577020"> <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>403</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9577020/"> Help finding proteases that most likely cleaved a peptide from a full-length protein </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/R/"> R </a> <a class="ptag" href="/tag/peptides/"> peptides </a> <a class="ptag" href="/tag/proteasix/"> proteasix </a> </div> <div class="right floated muted"> updated 40 minutes ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/cedce2f9/"> <span itemprop="name">Fatemeh</span> </a> ▴ 40 • written 18 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/137959/"> <span itemprop="name">georgiamorgannn</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9611110"> <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>35</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611110/"> protease candidates for my protein of interest </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/cleaving-site/"> cleaving-site </a> <a class="ptag" href="/tag/proteases/"> proteases </a> <a class="ptag" href="/tag/protein/"> protein </a> </div> <div class="right floated muted"> <span> 4 hours ago by <a href="/u/cedce2f9/"> Fatemeh </a> ▴ 40 </span> </div> </div> </div> </div> <div class="post open item" data-value="9611105"> <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>5</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>136</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611105/"> Which tools use or rely on the XA tag in SAM/BAM/CRAM files? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/cram/"> cram </a> <a class="ptag" href="/tag/XA/"> XA </a> <a class="ptag" href="/tag/compress/"> compress </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 6 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/9356/"> <span itemprop="name">Maarten</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9611100"> <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>54</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611100/"> Need Help Regarding Back-Splicing Junction Coordinates in CIRI2 Output </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/circRNA/"> circRNA </a> <a class="ptag" href="/tag/CIRI2/"> CIRI2 </a> </div> <div class="right floated muted"> updated 13 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 14 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149870/"> <span itemprop="name">Faraz</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9611091"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</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>78</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611091/"> Short reads to identify stuctural variants </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/SV/"> SV </a> <a class="ptag" href="/tag/long-read/"> long-read </a> <a class="ptag" href="/tag/short-read/"> short-read </a> </div> <div class="right floated muted"> updated 23 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/8494/"> <span itemprop="name">Ram</span> </a> <i class="ui muted bolt icon"></i> 45k • written 23 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/48330/"> <span itemprop="name">priya.bmg</span> </a> ▴ 70 </div> </div> </div> </div> <div class="post open item" data-value="9611088"> <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>162</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611088/"> Best approach for SNP calling in tumor single-cell multiome data (scRNA-seq + scATAC-seq) for CNV analysis </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/variant/"> variant </a> <a class="ptag" href="/tag/SNP/"> SNP </a> <a class="ptag" href="/tag/single-cell/"> single-cell </a> </div> <div class="right floated muted"> <span> 16 hours ago by <a href="/u/35890/"> nilaylale88 </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="9611080"> <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>3</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>168</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611080/"> C.reinhardtii single-cell Seurat object - gene names instead of loci </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/loci/"> loci </a> <a class="ptag" href="/tag/Chlamydomonas/"> Chlamydomonas </a> <a class="ptag" href="/tag/single-cell/"> single-cell </a> </div> <div class="right floated muted"> updated 23 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 1 day ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149753/"> <span itemprop="name">Ana</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9611072"> <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>3</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>137</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611072/"> Snakemake Global Environment Container </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/Snakemake/"> Snakemake </a> <a class="ptag" href="/tag/Conda/"> Conda </a> <a class="ptag" href="/tag/Singularity/"> Singularity </a> </div> <div class="right floated muted"> updated 5 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/71816/"> <span itemprop="name">DBScan</span> </a> ▴ 470 • written 1 day ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/145455/"> <span itemprop="name">meetmet</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9611068"> <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>100</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611068/"> GTF repeatmasker annotation file </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/repeatmasker/"> repeatmasker </a> <a class="ptag" href="/tag/GTF/"> GTF </a> </div> <div class="right floated muted"> <span> 1 day ago by <a href="/u/148587/"> frarodmar17 </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="9611062"> <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>105</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611062/"> How to select GEO datasets for differential expression analysis using GEO2R </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/GEO/"> GEO </a> <a class="ptag" href="/tag/DEGs/"> DEGs </a> <a class="ptag" href="/tag/GEO2R/"> GEO2R </a> </div> <div class="right floated muted"> updated 1 day 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 1 day ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149821/"> <span itemprop="name">dreamer247</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9590749"> <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>4</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>693</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9590749/"> PopGenome lost individual information </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/PopGenome/"> PopGenome </a> </div> <div class="right floated muted"> updated 1 day ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/22075/"> <span itemprop="name">Arup Ghosh</span> </a> <i class="ui muted bolt icon"></i> 3.3k • written 12 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/143645/"> <span itemprop="name">Yixuan</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9611045"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</div> </div> <div class="ui label stat mini question open bookmark"> <div>5</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>220</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611045/"> Polishing raw nanopore reads with Pacbio </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/polishing/"> polishing </a> <a class="ptag" href="/tag/assembly/"> assembly </a> </div> <div class="right floated muted"> <span> 19 hours ago by <a href="/u/44883/"> samuel.a.odonnell </a> ▴ 590 </span> </div> </div> </div> </div> <div class="post open item" data-value="9611026"> <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>6</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>260</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611026/"> Discrepancy between positions on IGV and NCBI's PrimerBLAST </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/igv/"> igv </a> <a class="ptag" href="/tag/primer/"> primer </a> <a class="ptag" href="/tag/blast/"> blast </a> </div> <div class="right floated muted"> <span> 3 hours ago by <a href="/u/60498/"> Rozita </a> ▴ 40 </span> </div> </div> </div> </div> <div class="post open item" data-value="9611025"> <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>151</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611025/"> Why does Radian run so much slower than vanilla R? </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/Radian/"> Radian </a> <a class="ptag" href="/tag/VS-Code/"> VS-Code </a> </div> <div class="right floated muted"> updated 22 hours ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/2/"> <span itemprop="name">Istvan Albert</span> </a> <i class="ui muted bolt icon"></i> 102k • written 2 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/148204/"> <span itemprop="name">RR</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9611023"> <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>95</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611023/"> Significant SNPs with the same effect in FarmCPU </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/effect-size/"> effect-size </a> <a class="ptag" href="/tag/gwas/"> gwas </a> <a class="ptag" href="/tag/FarmCPU/"> FarmCPU </a> <a class="ptag" href="/tag/likage-disequilibrium/"> likage-disequilibrium </a> </div> <div class="right floated muted"> <span> 2 days ago by <a href="/u/62468/"> AndrMod </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="9611010"> <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>113</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611010/"> rrvgo::getGoSize error </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/ReViGO/"> ReViGO </a> <a class="ptag" href="/tag/GO-terms/"> GO-terms </a> <a class="ptag" href="/tag/rrvgo/"> rrvgo </a> </div> <div class="right floated muted"> updated 1 day ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/8494/"> <span itemprop="name">Ram</span> </a> <i class="ui muted bolt icon"></i> 45k • written 2 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149753/"> <span itemprop="name">Ana</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9611009"> <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>109</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611009/"> Genotype Imputation for VCF File via API Using R ? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/Genotype-Imputation/"> Genotype-Imputation </a> <a class="ptag" href="/tag/VCF/"> VCF </a> <a class="ptag" href="/tag/API/"> API </a> </div> <div class="right floated muted"> <span> 2 days ago by <a href="/u/135822/"> Ahmed Jaber </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="9611002"> <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>127</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9611002/"> How label Group list after integratin scRNA-seq and scATAC-seq data </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/ArchR/"> ArchR </a> </div> <div class="right floated muted"> <span> 2 days ago by <a href="/u/143934/"> Bioinformatics_16 </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="9610988"> <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>7</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>459</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610988/"> Error in importing data from 10x genomics into RStudio </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/H5/"> H5 </a> <a class="ptag" href="/tag/file/"> file </a> <a class="ptag" href="/tag/scRNA/"> scRNA </a> <a class="ptag" href="/tag/RStudio/"> RStudio </a> </div> <div class="right floated muted"> <span> 1 day ago by <a href="/u/140322/"> himanshu0102 </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="9610992"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</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>236</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610992/"> WGS for CNV and Aneuploidy analysis </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/CNV/"> CNV </a> <a class="ptag" href="/tag/Aneuploidy/"> Aneuploidy </a> <a class="ptag" href="/tag/WGS/"> WGS </a> </div> <div class="right floated muted"> <span> 1 day ago by <a href="/u/149521/"> bioinfo1990 </a> ▴ 10 </span> </div> </div> </div> </div> <div class="post open item" data-value="9602536"> <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>546</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9602536/"> Issues with T2T in pigeon prepare from isoseq </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/long-read/"> long-read </a> <a class="ptag" href="/tag/isoseq/"> isoseq </a> <a class="ptag" href="/tag/rna-seq/"> rna-seq </a> </div> <div class="right floated muted"> updated 1 day ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/8494/"> <span itemprop="name">Ram</span> </a> <i class="ui muted bolt icon"></i> 45k • written 6 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/38001/"> <span itemprop="name">SethJ</span> </a> • 0 </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>299</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/crispr-screen/"> crispr-screen </a> <a class="ptag" href="/tag/batch-effect/"> batch-effect </a> <a class="ptag" href="/tag/correlation/"> correlation </a> </div> <div class="right floated muted"> updated 1 day ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/8494/"> <span itemprop="name">Ram</span> </a> <i class="ui muted bolt icon"></i> 45k • written 5 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/2295/"> <span itemprop="name">Assa Yeroslaviz</span> </a> ★ 1.9k </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>267</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 5 days 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 6 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/115665/"> <span itemprop="name">ohtang7</span> </a> ▴ 40 </div> </div> </div> </div> <div class="post open item" data-value="9610917"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</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>268</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610917/"> PCA comparison of cell line vs tumors </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/RNAseq/"> RNAseq </a> <a class="ptag" href="/tag/Sequencing/"> Sequencing </a> <a class="ptag" href="/tag/PCA/"> PCA </a> <a class="ptag" href="/tag/Normalization/"> Normalization </a> </div> <div class="right floated muted"> updated 2 days 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 6 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/146720/"> <span itemprop="name">karlensberg</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610913"> <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>200</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610913/"> Need help defining a threshold </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/DAVID/"> DAVID </a> <a class="ptag" href="/tag/Genes/"> Genes </a> <a class="ptag" href="/tag/GO/"> GO </a> </div> <div class="right floated muted"> <span> 6 days ago by <a href="/u/149753/"> Ana </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="9610892"> <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>212</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610892/"> How can I use mcmcglmm to calculate whether two traits are correlated? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/glmm/"> glmm </a> <a class="ptag" href="/tag/statistics/"> statistics </a> <a class="ptag" href="/tag/evolution/"> evolution </a> </div> <div class="right floated muted"> <span> 6 days ago by <a href="/u/106869/"> 雨 </a> ▴ 20 </span> </div> </div> </div> </div> <div class="post open item" data-value="9589811"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</div> </div> <div class="ui label stat mini question open bookmark"> <div>8</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>1.7k</div> <div>views</div> </div> <div class="subs">6 follow</div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9589811/"> FastQC on nanopore data: high proportion of polyA and polyG. Why ? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/fastQC/"> fastQC </a> <a class="ptag" href="/tag/polyG/"> polyG </a> <a class="ptag" href="/tag/ONT/"> ONT </a> <a class="ptag" href="/tag/nanopore/"> nanopore </a> <a class="ptag" href="/tag/polyA/"> polyA </a> </div> <div class="right floated muted"> updated 6 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/23882/"> <span itemprop="name">lieven.sterck</span> </a> <i class="ui muted bolt icon"></i> 15k • written 13 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/143381/"> <span itemprop="name">Matt</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610845"> <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>6</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>517</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610845/"> miRNA-seq normalization </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/miRDeep2/"> miRDeep2 </a> <a class="ptag" href="/tag/normalization/"> normalization </a> <a class="ptag" href="/tag/RNA-seq/"> RNA-seq </a> <a class="ptag" href="/tag/miRNA-seq/"> miRNA-seq </a> <a class="ptag" href="/tag/miRNA/"> miRNA </a> </div> <div class="right floated muted"> <span> 4 days ago by <a href="/u/95554/"> paulanavarrete116 </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="9610829"> <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>332</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610829/"> DEG analysys using pseudobulk from single cell RNA-seq </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/DEG/"> DEG </a> <a class="ptag" href="/tag/scRNA-seq/"> scRNA-seq </a> </div> <div class="right floated muted"> <span> 7 days ago by <a href="/u/111015/"> Diego </a> ▴ 110 </span> </div> </div> </div> </div> <div class="post open item" data-value="9610828"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</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>257</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610828/"> Microarray platform probrID to Circ-ID problem </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/CircRNA/"> CircRNA </a> <a class="ptag" href="/tag/microarray/"> microarray </a> </div> <div class="right floated muted"> updated 7 days 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 7 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149619/"> <span itemprop="name">ParastooA</span> </a> ▴ 20 </div> </div> </div> </div> <div class="post open item" data-value="9610827"> <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>4</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>379</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610827/"> Checking sex of a sample with sequencing data </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/ATAC-seq/"> ATAC-seq </a> </div> <div class="right floated muted"> <span> 6 days ago by <a href="/u/86394/"> xqyn </a> ▴ 30 </span> </div> </div> </div> </div> <div class="post open item" data-value="9610787"> <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>266</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610787/"> cant make the correct matrix </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/logfc/"> logfc </a> <a class="ptag" href="/tag/csv/"> csv </a> </div> <div class="right floated muted"> updated 8 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/23882/"> <span itemprop="name">lieven.sterck</span> </a> <i class="ui muted bolt icon"></i> 15k • written 8 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149152/"> <span itemprop="name">Naila</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610775"> <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>3</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>344</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610775/"> Assign different color in same section of Chord diagram in R </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/Chart/"> Chart </a> <a class="ptag" href="/tag/R/"> R </a> <a class="ptag" href="/tag/Diagram/"> Diagram </a> <a class="ptag" href="/tag/Plot/"> Plot </a> <a class="ptag" href="/tag/Chord/"> Chord </a> </div> <div class="right floated muted"> updated 7 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/36456/"> <span itemprop="name">Bastien Hervé</span> </a> <i class="ui muted bolt icon"></i> 6.2k • written 8 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/75144/"> <span itemprop="name">Jonathan Yoou</span> </a> ▴ 70 </div> </div> </div> </div> <div class="post open item" data-value="9610757"> <div class="stats"> <div class="ui mini stat left label"> <div>3</div> <div>votes</div> </div> <div class="ui label stat mini question open bookmark"> <div>8</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>458</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610757/"> Filter snRNA-seq .fastq files based on barcodes </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/snRNA-seq/"> snRNA-seq </a> <a class="ptag" href="/tag/scRNA-seq/"> scRNA-seq </a> <a class="ptag" href="/tag/FASTQ/"> FASTQ </a> <a class="ptag" href="/tag/bbmap/"> bbmap </a> </div> <div class="right floated muted"> updated 7 days 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 8 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/104026/"> <span itemprop="name">connorjfausto</span> </a> ▴ 30 </div> </div> </div> </div> <div class="post open item" data-value="9610754"> <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>156</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610754/"> Why is the IC50 of the low-risk group always lower than that of the high-risk group? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/OncoPredict/"> OncoPredict </a> </div> <div class="right floated muted"> <span> 8 days ago by <a href="/u/76012/"> nuorain </a> ▴ 40 </span> </div> </div> </div> </div> <div class="post open item" data-value="9610741"> <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>266</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610741/"> Remove batch effect RnaSeq (RUVg) </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/ruvg/"> ruvg </a> <a class="ptag" href="/tag/batch/"> batch </a> <a class="ptag" href="/tag/rnaseq/"> rnaseq </a> <a class="ptag" href="/tag/remove/"> remove </a> </div> <div class="right floated muted"> <span> 8 days ago by <a href="/u/146990/"> aLex97 </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="9610729"> <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>171</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610729/"> Annotation of CpG, DMRs and DMPs with MethylKit and Genomation in R </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/dmp/"> dmp </a> <a class="ptag" href="/tag/methylkit/"> methylkit </a> <a class="ptag" href="/tag/dmr/"> dmr </a> <a class="ptag" href="/tag/CpG/"> CpG </a> </div> <div class="right floated muted"> <span> 9 days ago by <a href="/u/144869/"> egascon </a> ▴ 60 </span> </div> </div> </div> </div> <div class="post open item" data-value="9610709"> <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/9610709/"> energy minimisation </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/Energy/"> Energy </a> </div> <div class="right floated muted"> updated 11 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 11 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149723/"> <span itemprop="name">swarnadurga66666m</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610708"> <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>285</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610708/"> How to concatenate different domains in the target database identified by hmmsearch </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/multiple/"> multiple </a> <a class="ptag" href="/tag/domains/"> domains </a> <a class="ptag" href="/tag/hmmsearch/"> hmmsearch </a> </div> <div class="right floated muted"> updated 11 days 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 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/10403/"> <span itemprop="name">Yongjie Zhang</span> </a> ▴ 110 </div> </div> </div> </div> <div class="post open item" data-value="9610707"> <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>284</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610707/"> How to filter Hmmsearch alignment </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/Hmmsearch/"> Hmmsearch </a> </div> <div class="right floated muted"> updated 10 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/56237/"> <span itemprop="name">Mensur Dlakic</span> </a> ★ 29k • written 11 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/10403/"> <span itemprop="name">Yongjie Zhang</span> </a> ▴ 110 </div> </div> </div> </div> <div class="post open item" data-value="9610695"> <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>395</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610695/"> Discrepancy between BAM and vcf </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/discrepancy/"> discrepancy </a> <a class="ptag" href="/tag/vcf/"> vcf </a> <a class="ptag" href="/tag/DRAGEN/"> DRAGEN </a> </div> <div class="right floated muted"> updated 11 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/2/"> <span itemprop="name">Istvan Albert</span> </a> <i class="ui muted bolt icon"></i> 102k • written 12 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/50221/"> <span itemprop="name">louis-gil</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610680"> <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>300</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610680/"> Reannotation of complete bacterial genome sequence </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/re-annotation/"> re-annotation </a> <a class="ptag" href="/tag/genome/"> genome </a> <a class="ptag" href="/tag/whole/"> whole </a> <a class="ptag" href="/tag/Automated/"> Automated </a> </div> <div class="right floated muted"> updated 9 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/12371/"> <span itemprop="name">Juke34</span> </a> <i class="ui muted bolt icon"></i> 9.2k • written 12 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/129478/"> <span itemprop="name">csag6433</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610678"> <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>885</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610678/"> What are the best tools for quantifying allele-specific expression from bulk RNA-seq data these days? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/ase/"> ase </a> <a class="ptag" href="/tag/phASER/"> phASER </a> <a class="ptag" href="/tag/allele/"> allele </a> <a class="ptag" href="/tag/gene/"> gene </a> <a class="ptag" href="/tag/gatk/"> gatk </a> </div> <div class="right floated muted"> updated 12 days 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 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/d3504e25/"> <span itemprop="name">Paulo</span> </a> ▴ 10 </div> </div> </div> </div> <div class="post open item" data-value="9610670"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</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>296</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610670/"> Mapping reversion mutations </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/NGS/"> NGS </a> <a class="ptag" href="/tag/reversion/"> reversion </a> <a class="ptag" href="/tag/mutation/"> mutation </a> </div> <div class="right floated muted"> updated 12 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/8494/"> <span itemprop="name">Ram</span> </a> <i class="ui muted bolt icon"></i> 45k • written 13 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149703/"> <span itemprop="name">reddyraghuveer664</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610668"> <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>228</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610668/"> Issue with Fetching Population Allele Frequency in gnomAD GraphQL API </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/allelle/"> allelle </a> <a class="ptag" href="/tag/frequency/"> frequency </a> <a class="ptag" href="/tag/api/"> api </a> <a class="ptag" href="/tag/GraphQL/"> GraphQL </a> <a class="ptag" href="/tag/gnomad/"> gnomad </a> </div> <div class="right floated muted"> <span> 13 days ago by <a href="/u/82465/"> DareDevil </a> ★ 4.4k </span> </div> </div> </div> </div> <div class="post open item" data-value="9610657"> <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>287</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610657/"> Attempts to demultiplex long reads from .pod5 result in unclassified reads </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/dorado/"> dorado </a> <a class="ptag" href="/tag/sequencing/"> sequencing </a> <a class="ptag" href="/tag/Long-read/"> Long-read </a> <a class="ptag" href="/tag/demultiplex/"> demultiplex </a> </div> <div class="right floated muted"> updated 13 days 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 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/112706/"> <span itemprop="name">Placeholder@12654926</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9610652"> <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>312</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610652/"> Issue with BSgenomeForge::forgeBSgenomeDataPkgFromNCBI </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/R/"> R </a> <a class="ptag" href="/tag/BSgenomeForge/"> BSgenomeForge </a> <a class="ptag" href="/tag/BSgenome/"> BSgenome </a> <a class="ptag" href="/tag/NCBI/"> NCBI </a> </div> <div class="right floated muted"> updated 13 days 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 13 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/55180/"> <span itemprop="name">noodle</span> </a> ▴ 650 </div> </div> </div> </div> <div class="post open item" data-value="9610651"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</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>321</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610651/"> Batch effect or biological difference </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/Batch-effect/"> Batch-effect </a> </div> <div class="right floated muted"> updated 12 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/8494/"> <span itemprop="name">Ram</span> </a> <i class="ui muted bolt icon"></i> 45k • written 13 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149694/"> <span itemprop="name">cynthier</span> </a> • 0 </div> </div> </div> </div> </div> <div class="ui page-bar segment"> <div class="ui small basic button no-shadow"> <i class="ui angle double left icon"> </i> </div> <span class="phone">1,000 results • Page </span> 1 of 20 <a class="ui small basic button no-shadow" href="/t/open/?page=2"> <i class="ui angle double right icon"></i> </a> </div> </div> <div class="four wide column sidefeed"> <div class="ui large wrap-text" id="sidebar"> <div class="event"> <div class="ui container"> <div class="title"> Recent Votes</div> <div class="ui relaxed list"> <div class="item spaced"> <a href="/p/9611058/"> <i class="thumbs up icon"></i> Comment: Methods for directional pathway analysis of DEGs?</a> </div> <div class="item spaced"> <a href="/p/9611099/"> <i class="thumbs up icon"></i> Answer: Methods for directional pathway analysis of DEGs?</a> </div> <div class="item spaced"> <a href="/p/9475538/"> <i class="thumbs up icon"></i> Answer: Adding Read Groups To Bam Files</a> </div> <div class="item spaced"> <a href="/p/9550142/"> <i class="thumbs up icon"></i> Prediction of Ribosomal RNA Genes Using RNAmmer Software</a> </div> <div class="item spaced"> <a href="/p/9585216/"> <i class="thumbs up icon"></i> Answer: salmon with long read</a> </div> <div class="item spaced"> <a href="/p/9585214/"> <i class="thumbs up icon"></i> salmon with long reads</a> </div> <div class="item spaced"> <a href="/p/308324/"> <i class="thumbs up icon"></i> Snpeff: clarification on gene fusion annotation</a> </div> </div> </div> </div> <div class="ui divider"></div> <div class="event"> <div class="ui container"> <div class="title">Recent Locations • <a href="/user/list/"> All <i class="ui angle small double right icon"></i></a> </div> <div class="ui relaxed list"> <div class="item spaced"> <span> <a class="ui mini avatar thread-users list-avatar image" href="/u/146720/"> <img src="https://secure.gravatar.com/avatar/286176bf4c2467fb267ea0b50018e332?s=90&d=mp"> </a> </span> United States, <span class="muted">just now</span> </div> <div class="item spaced"> <span> <a class="ui mini avatar thread-users list-avatar image" href="/u/111013/"> <img src="https://secure.gravatar.com/avatar/f8ffaf58b73139af370dc2145ab0610a?s=90&d=identicon"> </a> </span> United Kingdom, <span class="muted">just now</span> </div> <div class="item spaced"> <span> <a class="ui mini avatar thread-users list-avatar image" href="/u/29107/"> <img src="https://secure.gravatar.com/avatar/e258b420bcbc151f175cfb23cfcea135?s=90&d=robohash&f=y"> </a> </span> Germany, <span class="muted">1 minute ago</span> </div> <div class="item spaced"> <span> <a class="ui mini avatar thread-users list-avatar image" href="/u/40195/"> <img src="https://secure.gravatar.com/avatar/cd730167328ba9cc4b489e18570fd6eb?s=90&d=retro"> </a> </span> Memphis, TN, <span class="muted">2 minutes ago</span> </div> <div class="item spaced"> <span> <a class="ui mini avatar thread-users list-avatar image" href="/u/145620/"> <img src="https://secure.gravatar.com/avatar/87d96a1e5508dcbc0e6430eff02f0154?s=90&d=mp"> </a> </span> United States, <span class="muted">3 minutes ago</span> </div> <div class="item spaced"> <span> <a class="ui mini avatar thread-users list-avatar image" href="/u/149809/"> <img src="https://secure.gravatar.com/avatar/1ec1c6a60baa5257cd97d29cd2129b88?s=90&d=mp"> </a> </span> Russia, <span class="muted">4 minutes ago</span> </div> <div class="item spaced"> <span> <a class="ui mini avatar thread-users list-avatar image" href="/u/128580/"> <img src="https://secure.gravatar.com/avatar/b2cb79e4c6b9aae9f078bfc0b9a27b03?s=90&d=identicon"> </a> </span> Thailand, <span class="muted">5 minutes ago</span> </div> </div> </div> </div> <div class="ui divider"></div> <div class="event"> <div class="ui container"> <div class="title">Recent Awards • <a href="/b/list/"> All <i class="ui angle small double right icon"></i></a> </div> <div class="ui relaxed list"> <div class="item"> <span> <a href="/b/view/popular-question/"> <i class="eye icon"></i> Popular Question</a> to <a href="/u/73360/"> Neat</a> <span> • 0 </span> </span> </div> <div class="item"> <span> <a href="/b/view/popular-question/"> <i class="eye icon"></i> Popular Question</a> to <a href="/u/83915/"> GA</a> <span> • 0 </span> </span> </div> <div class="item"> <span> <a href="/b/view/popular-question/"> <i class="eye icon"></i> Popular Question</a> to <a href="/u/143197/"> Gerard</a> <span> ▴ 10 </span> </span> </div> <div class="item"> <span> <a href="/b/view/teacher/"> <i class="smile icon"></i> Teacher</a> to <a href="/u/8494/"> Ram</a> <span> <i class="ui muted bolt icon"></i> 45k </span> </span> </div> <div class="item"> <span> <a href="/b/view/popular-question/"> <i class="eye icon"></i> Popular Question</a> to <a href="/u/107794/"> Yuki _ISHIKAWA</a> <span> ▴ 20 </span> </span> </div> <div class="item"> <span> <a href="/b/view/teacher/"> <i class="smile icon"></i> Teacher</a> to <a href="/u/1149/"> Rob</a> <span> <i class="ui muted bolt icon"></i> 7.1k </span> </span> </div> <div class="item"> <span> <a href="/b/view/popular-question/"> <i class="eye icon"></i> Popular Question</a> to <a href="/u/62142/"> Begonia_pavonina</a> <span> ▴ 210 </span> </span> </div> </div> </div> </div> <div class="ui divider"></div> <div class="event"> <div class="ui container"> <div class="title">Recent Replies</div> <div class="ui relaxed list"> <div class="item spaced"> <a href="/p/9611125/"> Comment: Batch effect</a> by <a href="/u/cedce2f9/">Fatemeh </a> <span> ▴ 40 </span> <div class="muted"> I did not understand what do you mean by adding the batch in DESeq. Could you please explain more? Thanks very much. </div> </div> <div class="item spaced"> <a href="/p/9611123/"> Answer: Batch effect</a> by <a href="/u/4407/">swbarnes2 </a> <span> <i class="ui muted bolt icon"></i> 14k </span> <div class="muted"> Just add batch to the design in DESeq. But if your batch is confounded with an experimental condition, there is no magic trick to fix th… </div> </div> <div class="item spaced"> <a href="/p/9611122/"> Comment: Methods for directional pathway analysis of DEGs?</a> by <a href="/u/16790/">i.sudbery </a> <span> <i class="ui muted bolt icon"></i> 21k </span> <div class="muted"> While Gordon's answer is the technically correct one from a statistical point of view, please keep in mind that genes in a pathway being up… </div> </div> <div class="item spaced"> <a href="/p/9611121/"> Comment: Methods for directional pathway analysis of DEGs?</a> by <a href="/u/149846/">Steven </a> <span> • 0 </span> <div class="muted"> Thank you, I'll look into these functions, I appreciate it. If I have any follow ups, I'll comment here again. </div> </div> <div class="item spaced"> <a href="/p/9611120/"> Comment: Methods for directional pathway analysis of DEGs?</a> by <a href="/u/149846/">Steven </a> <span> • 0 </span> <div class="muted"> Ah thank you, this is pretty simple, I'm not sure why I didn't think of this. Thank you, I appreciate it! </div> </div> <div class="item spaced"> <a href="/p/9611119/"> 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"> Needs a summary :-) and TLDR: It looks like references with U do not work correctly with bowtie 1. </div> </div> <div class="item spaced"> <a href="/p/9611118/"> Comment: Which tools use or rely on the XA tag in SAM/BAM/CRAM files?</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> > Keeping this amount of data online in the cloud would cost 16K a year, so there is a bit of money True, but if you expect a number of pe… </div> </div> <div class="item spaced"> <a href="/p/9611117/"> Comment: Which tools use or rely on the XA tag in SAM/BAM/CRAM files?</a> by <a href="/u/9356/">Maarten </a> <span> • 0 </span> <div class="muted"> > Curious as to how you calculated this? I used [samtools cram-size][1] to calculate this. I already played around with genozip, and it … </div> </div> <div class="item spaced"> <a href="/p/9611115/"> Comment: Discrepancy between positions on IGV and NCBI's PrimerBLAST</a> by <a href="/u/60498/">Rozita </a> <span> ▴ 40 </span> <div class="muted"> Yes, I did. I entered the positions of the primers from PrimerBLAST in a CSV file then converted it to a BED file which opens successfully … </div> </div> <div class="item spaced"> <a href="/p/9611114/"> Comment: Which tools use or rely on the XA tag in SAM/BAM/CRAM files?</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> > files contain the optional XA:Z tag, which takes 22% of the total filesize Curious as to how you calculated this? If you are that wor… </div> </div> <div class="item spaced"> <a href="/p/9611113/"> Comment: Which tools use or rely on the XA tag in SAM/BAM/CRAM files?</a> by <a href="/u/9356/">Maarten </a> <span> • 0 </span> <div class="muted"> Thanks for the answer. I moved in experiments from cram 3.0 to cram 3.1 small,lossy_names=1. However, the compression of this block (gzip) … </div> </div> <div class="item spaced"> <a href="/p/9611112/"> Comment: Help finding proteases that most likely cleaved a peptide from a full-length pro</a> by <a href="/u/cedce2f9/">Fatemeh </a> <span> ▴ 40 </span> <div class="muted"> Hi Ram, Did you find any method for that? I am also having the same request. I could not open the website you suggested: http://www.proteas… </div> </div> <div class="item spaced"> <a href="/p/9611108/"> Comment: Which tools use or rely on the XA tag in SAM/BAM/CRAM files?</a> by <a href="/u/25721/">ATpoint </a> <span> <i class="ui muted bolt icon"></i> 87k </span> <div class="muted"> I can only strongly recommend to not mess with BAM files like this. At worst any downstream tool might simply check for presence of some ta… </div> </div> <div class="item spaced"> <a href="/p/9611107/"> Comment: Snakemake Global Environment Container</a> by <a href="/u/71816/">DBScan </a> <span> ▴ 470 </span> <div class="muted"> You can try to add `software-deployment-method: conda singularity` to you profile, this should work accordin to [https://snakemake.readthed… </div> </div> <div class="item spaced"> <a href="/p/9611106/"> Comment: Snakemake Global Environment Container</a> by <a href="/u/145455/">meetmet </a> <span> • 0 </span> <div class="muted"> Hello, I run snakemake from the main directory of the workflow: snakemake --profile workflow/profile --configfile .test/config/confi… </div> </div> </div> </div> </div> </div> </div> </div> <div id="traffic">Traffic: 2433 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>