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<html> <head> <title> Biostar Oma </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 " 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 " 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 ... 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data-value="9610275"> <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>11</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>669</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9610275/"> OMA use case </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/oma/"> oma </a> <a class="ptag" href="/tag/omastandalone/"> omastandalone </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 14 days ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/149571/"> <span itemprop="name">nmalexan</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9606577"> <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>978</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9606577/"> Is it possible to get the percentage identity between a pair of orthologs at the proteome level with the Orthology Matrix (OMA)? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/OMA/"> OMA </a> <a class="ptag" href="/tag/Sequence-identity/"> Sequence-identity </a> </div> <div class="right floated muted"> updated 3 months 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 3 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/148079/"> <span itemprop="name">fcampbel</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9600120"> <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>556</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9600120/"> Converting OMA IDs to Ensembl gene names </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/orthologs/"> orthologs </a> <a class="ptag" href="/tag/OMA/"> OMA </a> <a class="ptag" href="/tag/ensembl/"> ensembl </a> </div> <div class="right floated muted"> updated 8 months 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 8 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/146234/"> <span itemprop="name">Eric</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9597240"> <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>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>387</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9597240/"> Obtaining OMA and HOG IDs </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/OMA/"> OMA </a> <a class="ptag" href="/tag/browser/"> browser </a> </div> <div class="right floated muted"> updated 9 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/9877/"> <span itemprop="name">Adrian Altenhoff</span> </a> ★ 1.1k • written 9 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/145475/"> <span itemprop="name">gtzotzos</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9593460"> <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>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>475</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9593460/"> Finding orthologs between genome error </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/OMA/"> OMA </a> <a class="ptag" href="/tag/OMAbrowser/"> OMAbrowser </a> </div> <div class="right floated muted"> updated 11 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/9877/"> <span itemprop="name">Adrian Altenhoff</span> </a> ★ 1.1k • written 11 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/45628/"> <span itemprop="name">hemantcnaik</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9592130"> <div class="stats"> <div class="ui mini stat left label"> <div>0</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>2</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>446</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9592130/"> Mapping of OMA IDs to UniProtKB AC </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/OMA/"> OMA </a> <a class="ptag" href="/tag/orthologs/"> orthologs </a> </div> <div class="right floated muted"> updated 11 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/18713/"> <span itemprop="name">GenoMax</span> </a> <i class="ui muted bolt icon"></i> 150k • written 11 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/144039/"> <span itemprop="name">george</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9585748"> <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>518</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9585748/"> Errors from REST and Browser for specific HOGS? </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/OMA/"> OMA </a> </div> <div class="right floated muted"> <span> 14 months ago by <a href="/u/94992/"> Andrew </a> ▴ 20 </span> </div> </div> </div> </div> <div class="post open item" data-value="9575521"> <div class="stats"> <div class="ui mini stat left label"> <div>4</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>6</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>1.5k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9575521/"> OMA in AWS cloud </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/OMA/"> OMA </a> <a class="ptag" href="/tag/AWS/"> AWS </a> </div> <div class="right floated muted"> updated 17 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/9877/"> <span itemprop="name">Adrian Altenhoff</span> </a> ★ 1.1k • written 18 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/137284/"> <span itemprop="name">Ksel</span> </a> ▴ 10 </div> </div> </div> </div> <div class="post open item" data-value="9572002"> <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>2</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>1.0k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9572002/"> Retrieving Chromosome Accession for Specific Gene Using Ensembl REST API </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/OMA/"> OMA </a> <a class="ptag" href="/tag/Ensembl/"> Ensembl </a> <a class="ptag" href="/tag/Rest/"> Rest </a> </div> <div class="right floated muted"> updated 20 months 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 20 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/104181/"> <span itemprop="name">Nicolas</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9571632"> <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>3</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>769</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9571632/"> Downloading Microsyntenic Fasta Sequences with Varying Chromosome Formats </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/microsyntenic-region/"> microsyntenic-region </a> <a class="ptag" href="/tag/fasta/"> fasta </a> <a class="ptag" href="/tag/oma/"> oma </a> <a class="ptag" href="/tag/chromosomes/"> chromosomes </a> </div> <div class="right floated muted"> <span> 20 months ago by <a href="/u/104181/"> Nicolas </a> • 0 </span> </div> </div> </div> </div> <div class="post open item" data-value="9570357"> <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>11</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>2.0k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9570357/"> search for intron conservancy across species </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/intron/"> intron </a> <a class="ptag" href="/tag/oma/"> oma </a> <a class="ptag" href="/tag/intronDB/"> intronDB </a> <a class="ptag" href="/tag/splicing/"> splicing </a> </div> <div class="right floated muted"> <span> 20 months ago by <a href="/u/25100/"> Buffo </a> ★ 2.4k </span> </div> </div> </div> </div> <div class="post open item" data-value="9569114"> <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>1.2k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9569114/"> oma orthology part 2 script </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/oma/"> oma </a> <a class="ptag" href="/tag/orthologous-groups/"> orthologous-groups </a> <a class="ptag" href="/tag/orthology/"> orthology </a> </div> <div class="right floated muted"> updated 20 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/119287/"> <span itemprop="name">Silvia Prieto</span> </a> ▴ 30 • written 21 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/134438/"> <span itemprop="name">kylakell</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9566505"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</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>1.3k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Job: <a href="/p/9566505/"> Postdoctoral position in Evolutionary Structural Bioinformatics </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/urmetazoan/"> urmetazoan </a> <a class="ptag" href="/tag/OMA/"> OMA </a> <a class="ptag" href="/tag/phylogenetics/"> phylogenetics </a> <a class="ptag" href="/tag/common-ancestor/"> common-ancestor </a> </div> <div class="right floated muted"> updated 21 months 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 21 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/44557/"> <span itemprop="name">sina.majidian</span> </a> ▴ 20 </div> </div> </div> </div> <div class="post open item" data-value="9566504"> <div class="stats"> <div class="ui mini stat left label"> <div>1</div> <div>vote</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>1.3k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> Job: <a href="/p/9566504/"> Postdoctoral Research position in Bioinformatics and Comparative Genomics </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/Genomics/"> Genomics </a> <a class="ptag" href="/tag/OMA/"> OMA </a> <a class="ptag" href="/tag/synteny/"> synteny </a> <a class="ptag" href="/tag/ancestral/"> ancestral </a> </div> <div class="right floated muted"> updated 21 months 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 21 months ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/44557/"> <span itemprop="name">sina.majidian</span> </a> ▴ 20 </div> </div> </div> </div> <div class="post open item" data-value="9558878"> <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>8</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>1.6k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9558878/"> syntax errors when running part3 all-against-all </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/oma/"> oma </a> </div> <div class="right floated muted"> <span> 2.0 years ago by <a href="/u/126958/"> Sofia </a> ▴ 10 </span> </div> </div> </div> </div> <div class="post open item" data-value="9553252"> <div class="stats"> <div class="ui mini stat left label"> <div>4</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>2</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>1.0k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9553252/"> Obtaining every"Protein ID" from a genome in OMA </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/OMA/"> OMA </a> <a class="ptag" href="/tag/orthologs/"> orthologs </a> </div> <div class="right floated muted"> updated 2.2 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/9877/"> <span itemprop="name">Adrian Altenhoff</span> </a> ★ 1.1k • written 2.2 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/123127/"> <span itemprop="name">christyh</span> </a> ▴ 10 </div> </div> </div> </div> <div class="post open item" data-value="9553346"> <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>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>648</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9553346/"> Error, (in LoadSpliceMap) string to parse is too long </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/oma/"> oma </a> <a class="ptag" href="/tag/LoadSpliceMap/"> LoadSpliceMap </a> <a class="ptag" href="/tag/omastandalone/"> omastandalone </a> <a class="ptag" href="/tag/orthology/"> orthology </a> </div> <div class="right floated muted"> updated 2.2 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/9877/"> <span itemprop="name">Adrian Altenhoff</span> </a> ★ 1.1k • written 2.2 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/118330/"> <span itemprop="name">ziqing</span> </a> ▴ 10 </div> </div> </div> </div> <div class="post open item" data-value="9548452"> <div class="stats"> <div class="ui mini stat left label"> <div>4</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers open bookmark"> <div>2</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>966</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9548452/"> OMA standalone error during database conversion step: Matches 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data-value="9523333"> <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>877</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9523333/"> Orthologs distances in OMA </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/OMA/"> OMA </a> <a class="ptag" href="/tag/orthologs/"> orthologs </a> </div> <div class="right floated muted"> updated 2.9 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/9877/"> <span itemprop="name">Adrian Altenhoff</span> </a> ★ 1.1k • written 2.9 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/42254/"> <span itemprop="name">Abel Sousa</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9520683"> <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>1</div> <div>reply</div> </div> <div class="ui label basic transparent stat mini"> <div>678</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9520683/"> Multiple OMA groups per uniprotID in OMAdb </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/OMA/"> OMA </a> <a class="ptag" href="/tag/orthologs/"> orthologs </a> </div> <div class="right floated muted"> updated 2.9 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/9877/"> <span itemprop="name">Adrian Altenhoff</span> </a> ★ 1.1k • written 2.9 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/108567/"> <span itemprop="name">chow</span> </a> ▴ 10 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1.1k • written 3.1 years ago by <a itemprop="author" itemscope itemtype="https://schema.org/Person" href="/u/105478/"> <span itemprop="name">pragyadeeproy</span> </a> • 0 </div> </div> </div> </div> <div class="post open item" data-value="9506368"> <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>1.1k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/9506368/"> Evolutionary dynamics with OMAmer HOGs (orthoXML file?) </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/orthologs/"> orthologs </a> <a class="ptag" href="/tag/OMAmer/"> OMAmer </a> <a class="ptag" href="/tag/HOGs/"> HOGs </a> <a class="ptag" href="/tag/oma/"> oma </a> <a class="ptag" href="/tag/pyHAM/"> pyHAM </a> </div> <div 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</a> <a class="ptag" href="/tag/error/"> error </a> </div> <div class="right floated muted"> <span> 4.3 years ago by <a href="/u/49135/"> m3hdad </a> ▴ 10 </span> </div> </div> </div> </div> <div class="post open item" data-value="477881"> <div class="stats"> <div class="ui mini stat left label"> <div>12</div> <div>votes</div> </div> <div class="ui label stat mini question has_answers accepted answer bookmark"> <div>11</div> <div>replies</div> </div> <div class="ui label basic transparent stat mini"> <div>2.0k</div> <div>views</div> </div> </div> <div class="content"> <div class="title mini header"> <a href="/p/477881/"> Error running OMA standalone at HOG computation step </a> </div> <div class="extra right floated"> <div class="left floated"> <a class="ptag" href="/tag/OMA/"> OMA </a> <a class="ptag" href="/tag/HOG/"> HOG </a> <a class="ptag" href="/tag/error/"> error </a> <a class="ptag" href="/tag/orthologs/"> orthologs </a> </div> <div class="right floated muted"> updated 4.3 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You can try writing to Brian Bushnell (his email can be found in software i… </div> </div> <div class="item spaced"> <a href="/p/9610834/"> Comment: Alternatives to UCSC genome browser for obtaining gene coordinates</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> Get the basic gene annotation from https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_47/GRCh37_mapping/gencode.v47lift37.ba… </div> </div> <div class="item spaced"> <a href="/p/9610833/"> Comment: bbduk.sh trimming to BAM output file</a> by <a href="/u/149756/">bge </a> <span> • 0 </span> <div class="muted"> Hi, I appreciate the confirmation -- I worry that I mess up. Anyway, the input uBAM file has a tag with the barcode+umi sequences req… </div> </div> <div class="item spaced"> <a href="/p/9610831/"> Comment: Microarray platform probrID to Circ-ID problem</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> This appears to be a commercially available array. You could contact Arraystar and see if they would be willing to share the annotations: h… </div> </div> <div class="item spaced"> <a href="/p/9610830/"> Answer: bbduk.sh trimming to BAM output file</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> Using a uBAM input and writing uBAM output is indeed not working directly. Probably because it is an edge case that @Brian likely did not t… </div> </div> <div class="item spaced"> <a href="/p/9610824/"> Comment: Filter snRNA-seq .fastq files based on barcodes</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> Use the 10x's BAM splitting tool (https://github.com/10XGenomics/subset-bam ). You should share those BAM's (instead of fastq) since they h… </div> </div> <div class="item spaced"> <a href="/p/9610823/"> Comment: Filter snRNA-seq .fastq files based on barcodes</a> by <a href="/u/104026/">connorjfausto </a> <span> ▴ 30 </span> <div class="muted"> > What is the intent behind doing this? From our original snRNA-seq Seurat object, we have a small subset (~5% of nuclei) that collaborato… </div> </div> <div class="item spaced"> <a href="/p/9610822/"> Comment: Batch correction RNA-seq analysis</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> Since you are stuck with what you have keep this is as another variable (hopefully it is same as two sequencer batches). Generally people (… </div> </div> <div class="item spaced"> <a href="/p/9610821/"> Comment: Batch correction RNA-seq analysis</a> by <a href="/u/149754/">ka132 </a> <span> • 0 </span> <div class="muted"> Unfortunately, I just found out the libraries were prepped separately as well. Thanks for the advice! </div> </div> <div class="item spaced"> <a href="/p/9610820/"> Comment: Batch correction RNA-seq analysis</a> by <a href="/u/149754/">ka132 </a> <span> • 0 </span> <div class="muted"> Well, dangit - I just heard back and the same sequencer was used but library prep was done separately. Bummer. Thanks for the assistance. </div> </div> <div class="item spaced"> <a href="/p/9610819/"> Comment: Batch correction RNA-seq analysis</a> by <a href="/u/40195/">jared.andrews07 </a> <span> ★ 18k </span> <div class="muted"> Batch correction as you mention shouldn't even run, I expect ComBat-seq will yell at you about confounded covariates if you try. But as me… </div> </div> <div class="item spaced"> <a href="/p/9610818/"> Comment: Batch correction RNA-seq analysis</a> by <a href="/u/149754/">ka132 </a> <span> • 0 </span> <div class="muted"> The actual experiment and collection of samples were done at same time. Library prep was definitely done by same person using same protocol… </div> </div> <div class="item spaced"> <a href="/p/9610817/"> Comment: Batch correction RNA-seq analysis</a> by <a href="/u/18713/">GenoMax </a> <span> <i class="ui muted bolt icon"></i> 150k </span> <div class="muted"> There should be no appreciable batch effect because of sequencing, as long as following is true. The same sequencer (or at least type i.e. … </div> </div> <div class="item spaced"> <a href="/p/9610816/"> Comment: Batch correction RNA-seq analysis</a> by <a href="/u/149754/">ka132 </a> <span> • 0 </span> <div class="muted"> yeah.... this is what I was afraid of. I wish this was a lesson that I needed to learn, but again I had no input on the processing up to th… </div> </div> <div class="item spaced"> <a href="/p/9610815/"> Comment: Batch correction RNA-seq analysis</a> by <a href="/u/149754/">ka132 </a> <span> • 0 </span> <div class="muted"> Just sequencing, no common control unfortunately. </div> </div> </div> </div> </div> </div> </div> </div> <div id="traffic">Traffic: 1546 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>