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Ultrafast functional profiling of RNA-seq data for nonmodel organisms — Supplemental Material

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /> <title>Ultrafast functional profiling of RNA-seq data for nonmodel organisms — Supplemental Material </title> <meta name="googlebot" content="NOODP" /> <meta name="description" content="An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms" /> <link rel="stylesheet" type="text/css" media="all" href="/shared/css/hw-global.css" /> <link rel="stylesheet" type="text/css" media="all" href="/shared/css/standard-designs/design2/main.css" /> <link rel="stylesheet" type="text/css" media="all" href="/publisher/css/hw-cshljnls-global.css" /> <link rel="stylesheet" type="text/css" media="all" href="/local/css/hw-journal-global.css" /> <link rel="stylesheet" type="text/css" media="all" href="/shared/css/hw-citation-2.0-hacks.css" /> <link rel="stylesheet" type="text/css" media="print" href="/shared/css/hw-print.css" /> <link rel="stylesheet" type="text/css" media="print" href="/publisher/css/hw-cshljnls-print.css" /> <link rel="stylesheet" type="text/css" media="all" href="/shared/css/hw-page-content.css" /> <link rel="stylesheet" type="text/css" media="all" href="/shared/css/hw-page-data-supp.css" /> <link rel="stylesheet" type="text/css" media="all" href="/publisher/css/hw-cshljnls-page-content.css" /> <link rel="stylesheet" type="text/css" media="all" href="/site/misc/custom-global.css" /><script type="text/javascript" id="session-d9271150e1">var callbackToken='515095D40278DB5';</script><script type="text/javascript" src="/shared/js/jquery-min.js"></script><script type="text/javascript" src="/shared/js/fingerprint.js"></script><script type="text/javascript" src="/shared/js/hw-shared.js"></script><script type="text/javascript" src="/shared/js/design/hw-design1.js"></script><script type="text/javascript" src="/publisher/js/cshl-shared.js"></script><script type="text/javascript" src="/site/misc/custom-global.js"></script></head> <body> <div class="hw-gen-page pagetype-content" id="pageid-data-supp"> <div id="header"> <a href="http://www.cshlpress.com" rel="external-nw"><img src="/local/img/society_logo.gif" width="74" height="83" alt="Publisher Logo" id="main-logo" /></a><a href="/"><img title="Genome Research" alt="Genome Research" width="313" height="83" src="/local/img/journal_logo_standalone.gif" /></a> <p id="skip-link"> <a href="#content-block">Skip to main page content</a> </p> <ul class="button-list header-buttons"> <li class="first"><a href="/" title="HOME"><span>HOME</span></a></li> <li><a href="/site/misc/about.xhtml" title="ABOUT"><span>ABOUT</span></a></li> <li><a href="/content/by/year" title="ARCHIVE"><span>ARCHIVE</span></a></li> <li><a href="http://submit.genome.org/" title="SUBMIT"><span>SUBMIT</span></a></li> <li><a href="/site/subscriptions/" title="SUBSCRIBE"><span>SUBSCRIBE</span></a></li> <li><a href="/site/misc/adinfo.xhtml" title="ADVERTISE"><span>ADVERTISE</span></a></li> <li><a href="/site/misc/ifora.xhtml" title="AUTHOR INFO"><span>AUTHOR INFO</span></a></li> <li><a href="/feedback" title="CONTACT"><span>CONTACT</span></a></li> <li class="last"><a href="/help/" title="HELP"><span>HELP</span></a></li> </ul> <div class="header-qs"> <form class="searchbox" action="/search" method="get"> <div> <label for="header-qs-input" id="header-qs-search-label">Search for Keyword:</label> <input value="" title="Search Genome Research" type="text" name="fulltext" id="header-qs-input" /><input type="hidden" name="submit" value="yes" /><label for="header-qs-search" id="header-qs-search-label">GO</label><input value="GO" alt="Link: Go" type="image" id="header-qs-search-go" src="/shared/img/standard-design/design2/go.gif" /> </div> <div class="adv-search-link"><a href="/search">Advanced Search</a></div> </form> </div> <div class="header-ac-elements"> <div class="inst-branding"> </div> <div id="authstring" class="suppress-header-login"> </div> <div id="hdr-login" class="suppress-header-login"></div> </div> <div class="banner-ads"> <ul> <li><a href="/cgi/adclick/?ad=57883&amp;adclick=true&amp;url=https%3A%2F%2Fprograms.pacb.com%2Fl%2F1652%2F2024-10-14%2F44v4m7" target="_blank"><img class="adborder0" title="PacBio" src="//genome.cshlp.org/adsystem/graphics/5504699488250983/genome/PacBio%20LB%20Accuracy.jpg?ad=57883&amp;adview=true" alt="PacBio" /></a></li> </ul> </div> <div class="bar"> <div class="bar-inner"></div> </div> </div> <div id="content-block"> <h1 class="data-supp-article-title">Ultrafast functional profiling of RNA-seq data for nonmodel organisms</h1> <div><span class="highwire-journal-article-marker-start"></span><div class="auto-clean"><span style="font-family: Verdana,Arial,Helvetica,sans-serif; font-size: 83.33%"> <h2>Supplemental Material</h2> <ul> <li><a href="/content/suppl/2021/03/17/gr.269894.120.DC1/Supplemental_Code.zip">Supplemental_Code.zip</a> </li> <li><a href="/content/suppl/2021/03/17/gr.269894.120.DC1/Supplemental_Materials.docx">Supplemental_Materials.docx</a> </li> </ul> </span> </div><span class="highwire-journal-article-marker-end"></span></div><span id="related-urls"></span><div id="content-end-sb" class="sb-div"></div> </div> <div id="col-2"> <div class="content-box" id="article-cb-main"> <div class="cb-contents"> <h3 class="cb-contents-header"><span>This Article</span></h3> <div class="cb-section cb-slug"> <ol> <li> <div id="slugline"> <span class="slug-metadata-note ahead-of-print"> Published in Advance <span class="slug-ahead-of-print-date">March 17, 2021</span>, doi: <span title="10.1101/gr.269894.120" class="slug-doi">10.1101/gr.269894.120</span> </span> <cite> <abbr title="Genome Research" class="slug-jnl-abbrev"> Genome Res.</abbr><span class="slug-pub-date"> April 2021 </span> <span class="slug-vol"> vol. 31 </span><span class="slug-issue"> no. 4 </span><span class="slug-pages"> 713-720 </span> </cite> </div> </li> </ol> </div> <div class="cb-section"> <ol> <li><a href="/content/31/4/713.abstract" rel="view-abstract">Abstract</a><span class="free">Free</span></li> <li class="notice"><a href="/content/31/4/713.full" rel="view-full-text">Full Text</a><span class="free">Free</span></li> <li class="notice"><a href="/content/31/4/713.full.pdf+html" rel="view-full-text.pdf">Full Text (PDF)</a></li> <li><span class="variant-indicator">» <span>Supplemental Material</span></span></li> </ol> </div> </div> </div> <div class="content-box" id="art-history-pane"> <div class="cb-contents"> <div class="cb-section collapsible default-closed" id="cb-art-gs"> <h4 class="cb-section-header"> <span>Preprint Server</span> </h4> <div id="art-history"></div> </div> </div> </div> <div class="content-box" id="article-cb-main"> <div class="cb-contents"> <div class="cb-section collapsible default-closed" id="cb-art-gs-cshl"></div> </div> </div> <div id="col-2-widget-placeholder"> <br /> <br /> </div> <ul class="tower-ads"> <li class="no-ad tower_col_2"><span> </span></li> </ul> </div> <div id="col-3"> <div class="content-box" id="sidebar-current-issue"> <div class="cb-contents"> <h3 class="cb-contents-header"><span>Current Issue</span></h3> <div class="cb-section"> <ol> <li><span><a href="/content/current" rel="current-issue">November 2024, 34 (11)</a></span></li> </ol> </div> <div class="cb-section"> <ol> <li> <div class="current-issue"><a href="/content/current" rel="current-issue"><img src="/content/34/11.cover.gif" width="67" height="89" alt="Current Issue" /></a></div> </li> </ol> </div> <cb:item xmlns:cb="http://schema.highwire.org/Site/Content-Box"> <div class="cb-section collapsible default-closed" id="sidebar-cur-issue-coverlines"> <h4 class="cb-section-header"> <span>From the Cover</span> </h4> <ul> <li> <a href="/site/cl/CL_34_11_dis_canc.xhtml">Rare disease and cancer genomics</a> </li> <li> <a href="/site/cl/CL_34_11_long_read.xhtml">Long-read RNA sequencing</a> </li> <li> <a href="/site/cl/CL_34_11_chrom_lev.xhtml">T2T and chromosome-level assemblies</a> </li> <li> <a href="/site/cl/CL_34_11_data_app.xhtml">Novel long-read sequencing data approaches</a> </li> <li> <a href="/site/cl/CL_34_11_det_char.xhtml">Rapid pathogen detection and characterization</a> </li> </ul> </div> </cb:item> <div class="cb-section sidebar-etoc-link"> <ol> <li><a href="/cgi/alerts/etoc">Alert me to new issues of <span class="journal-name"> Genome Research </span> </a></li> </ol> </div> </div> </div> <div id="sidebar-global-nav"> <ul class="button-list pub-links"> <li class="first"><a href="/content/early/recent" title="Advance Online Articles "><span>Advance Online Articles </span></a></li> <li><a href="http://submit.genome.org/" rel="external-nw" title="Submit a Manuscript"><span>Submit a Manuscript</span></a></li> <li><a href="/site/press/Announcements.xhtml" title="GR in the News "><span>GR in the News </span></a></li> <li><a href="/site/misc/about.xhtml" title="Editorial Board"><span>Editorial Board</span></a></li> <li><a href="/site/misc/permissions_landing.xhtml" title="Permissions"><span>Permissions</span></a></li> <li><a href="/site/misc/alertland.xhtml" title="E-mail Alerts &amp; 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