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| author | petr-novak |
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| date | Thu, 19 Dec 2019 10:24:45 -0500 |
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<?xml version="1.0" encoding="utf-8"?> <!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" lang="en" xml:lang="en"> <head> <!-- 2016-10-21 Pá 11:06 --> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta name="viewport" content="width=device-width, initial-scale=1" /> <title>TAREAN output description</title> <meta name="generator" content="Org-mode" /> <meta name="author" content="petr" /> <style type="text/css"> <!--/*--><![CDATA[/*><!--*/ .title { text-align: center; margin-bottom: .2em; } .subtitle { text-align: center; font-size: medium; font-weight: bold; margin-top:0; } .todo { font-family: monospace; color: red; } .done { font-family: monospace; color: green; } .priority { font-family: monospace; color: orange; } .tag { background-color: #eee; font-family: monospace; padding: 2px; font-size: 80%; font-weight: normal; } .timestamp { color: #bebebe; } .timestamp-kwd { color: #5f9ea0; } .org-right { margin-left: auto; margin-right: 0px; text-align: right; } .org-left { margin-left: 0px; margin-right: auto; text-align: left; } .org-center { margin-left: auto; margin-right: auto; text-align: center; } .underline { text-decoration: underline; } #postamble p, #preamble p { font-size: 90%; margin: .2em; } p.verse { margin-left: 3%; } pre { border: 1px solid #ccc; box-shadow: 3px 3px 3px #eee; padding: 8pt; font-family: monospace; overflow: auto; margin: 1.2em; } pre.src { position: relative; overflow: visible; padding-top: 1.2em; } pre.src:before { display: none; position: absolute; background-color: white; top: -10px; right: 10px; padding: 3px; border: 1px solid black; } pre.src:hover:before { display: inline;} pre.src-sh:before { content: 'sh'; } pre.src-bash:before { content: 'sh'; } pre.src-emacs-lisp:before { content: 'Emacs Lisp'; } pre.src-R:before { content: 'R'; } pre.src-perl:before { content: 'Perl'; } pre.src-java:before { content: 'Java'; } pre.src-sql:before { content: 'SQL'; } table { border-collapse:collapse; } caption.t-above { caption-side: top; } caption.t-bottom { caption-side: bottom; } td, th { vertical-align:top; } th.org-right { text-align: center; } th.org-left { text-align: center; } th.org-center { text-align: center; } td.org-right { text-align: right; } td.org-left { text-align: left; } td.org-center { text-align: center; } dt { font-weight: bold; } .footpara { display: inline; } .footdef { margin-bottom: 1em; } .figure { padding: 1em; } .figure p { text-align: center; } .inlinetask { padding: 10px; border: 2px solid gray; margin: 10px; background: #ffffcc; } #org-div-home-and-up { text-align: right; font-size: 70%; white-space: nowrap; } textarea { overflow-x: auto; } .linenr { font-size: smaller } .code-highlighted { background-color: #ffff00; } .org-info-js_info-navigation { border-style: none; } #org-info-js_console-label { font-size: 10px; font-weight: bold; white-space: nowrap; } .org-info-js_search-highlight { background-color: #ffff00; color: #000000; font-weight: bold; } /*]]>*/--> </style> <link rel="stylesheet" type="text/css" href="style1.css" /> <script type="text/javascript"> /* @licstart The following is the entire license notice for the JavaScript code in this tag. Copyright (C) 2012-2013 Free Software Foundation, Inc. The JavaScript code in this tag is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License (GNU GPL) as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. The code is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU GPL for more details. As additional permission under GNU GPL version 3 section 7, you may distribute non-source (e.g., minimized or compacted) forms of that code without the copy of the GNU GPL normally required by section 4, provided you include this license notice and a URL through which recipients can access the Corresponding Source. @licend The above is the entire license notice for the JavaScript code in this tag. */ <!--/*--><![CDATA[/*><!--*/ function CodeHighlightOn(elem, id) { var target = document.getElementById(id); if(null != target) { elem.cacheClassElem = elem.className; elem.cacheClassTarget = target.className; target.className = "code-highlighted"; elem.className = "code-highlighted"; } } function CodeHighlightOff(elem, id) { var target = document.getElementById(id); if(elem.cacheClassElem) elem.className = elem.cacheClassElem; if(elem.cacheClassTarget) target.className = elem.cacheClassTarget; } /*]]>*///--> </script> </head> <body> <div id="content"> <h1 class="title">TAREAN output description</h1> <div id="table-of-contents"> <h2>Table of Contents</h2> <div id="text-table-of-contents"> <ul> <li><a href="#orgheadline1">1. Introduction</a></li> <li><a href="#orgheadline3">2. Main HTML report</a> <ul> <li><a href="#orgheadline2">2.1. Table legend</a></li> </ul> </li> <li><a href="#orgheadline5">3. Detailed cluster report</a> <ul> <li><a href="#orgheadline4">3.1. Table legend</a></li> </ul> </li> <li><a href="#orgheadline7">4. Structure of the output archive</a> <ul> <li><a href="#orgheadline6">4.1. structure of cluster directories</a></li> </ul> </li> </ul> </div> </div> <div id="outline-container-orgheadline1" class="outline-2"> <h2 id="orgheadline1"><span class="section-number-2">1</span> Introduction</h2> <div class="outline-text-2" id="text-1"> <p> TAREAN output includes <b>HTML report</b> with list of all analyzed clusters; the clusters are classified into five categories: </p> <ul class="org-ul"> <li>high confidence satellites</li> <li>low confidence satellites</li> <li>potential LTR elements</li> <li>rDNA</li> <li>other clusters</li> </ul> <p> Each cluster for which consensus sequences was reconstructed has also its own detailed report, linked to the main report. </p> </div> </div> <div id="outline-container-orgheadline3" class="outline-2"> <h2 id="orgheadline3"><span class="section-number-2">2</span> Main HTML report</h2> <div class="outline-text-2" id="text-2"> <p> This report contains basic information about all clusters larger than specified threshold (default value is 0.01% of analyzed reads) </p> </div> <div id="outline-container-orgheadline2" class="outline-3"> <h3 id="orgheadline2"><span class="section-number-3">2.1</span> Table legend</h3> <div class="outline-text-3" id="text-2-1"> <dl class="org-dl"> <dt>Cluster</dt><dd>Cluster identifier</dd> <dt>Genome Proportion<code>[%]</code></dt><dd><i>(Number of sequences in cluster/Number of sequences in clustering) x 100%</i></dd> <dt>Size</dt><dd>Number of reads in the cluster</dd> <dt>Satellite probability</dt><dd>Empirical probability estimate that cluster sequences are derived from satellite repeat. This estimate is based on analysis of more than xxx clusters including yyy manually anotated and zzz experimentaly validated satellite repeats</dd> <dt>Consensus</dt><dd>Consensus sequence is outcome of kmer-based analysis and represents the most probable satellite monomer sequence</dd> <dt>Kmer analysis</dt><dd>link to analysis report for individual clusters</dd> <dt>Graph layout</dt><dd>Graph-based visualization of similarities among sequence reads</dd> <dt>Connected component index</dt><dd>Proportion of nodes of the graph which are part of the the largest strongly connected component</dd> <dt>Pair completeness index</dt><dd>Proportion of reads with available mate-pair within the same cluster</dd> <dt>Kmer coverage</dt><dd>Sum of relative frequencies of all kmers used for consensus sequence reconstruction</dd> <dt>|V|</dt><dd>Number of vertices of the graph</dd> <dt>|E|</dt><dd>Number of edges of the graph</dd> <dt>PBS score</dt><dd>Primer binding site detection score</dd> <dt>The longest ORF length</dt><dd>Length of the longest open reading frame found in any of the possible six reading frames. Search was done on dimer of consensus so ORFs can be longer than 'monomer' length</dd> <dt>Similarity-based annotation</dt><dd>Annotation based on similarity search using blastn/blastx against database of known repeats.</dd> </dl> </div> </div> </div> <div id="outline-container-orgheadline5" class="outline-2"> <h2 id="orgheadline5"><span class="section-number-2">3</span> Detailed cluster report</h2> <div class="outline-text-2" id="text-3"> <p> Cluster report includes a list of major monomer sequence varinats reconstructed from the most frequent k-mers. The reconstructed consensus sequences are sorted based on their significance (that is, what proportion of k-mer they represent). </p> </div> <div id="outline-container-orgheadline4" class="outline-3"> <h3 id="orgheadline4"><span class="section-number-3">3.1</span> Table legend</h3> <div class="outline-text-3" id="text-3-1"> <dl class="org-dl"> <dt>kmer</dt><dd>length of kmer used for consensus reconstruction.</dd> <dt>variant</dt><dd>identifier of consensus variant.</dd> <dt>total score</dt><dd>measure of significance of consensus variant. Score is calculated as a sum of weights of all k-mers used for consensus reconstruction.</dd> <dt>monomer length</dt><dd>length of the consensus</dd> <dt>consensus</dt><dd>consensus sequence without ambiguous bases.</dd> <dt>graph image</dt><dd>part of de-Bruijn graph based on the abundant k-mers. Size of vertices corresponds to k-mer frequencies, Paths in the graph which was used for reconstruction of consensus sequences is gray colored.</dd> <dt>logo image</dt><dd>consensus sequences shown as DNA logo. Height of letters corresponds to kmer frequencies. Logo images are linked to corresponding position probability matrices.</dd> </dl> </div> </div> </div> <div id="outline-container-orgheadline7" class="outline-2"> <h2 id="orgheadline7"><span class="section-number-2">4</span> Structure of the output archive</h2> <div class="outline-text-2" id="text-4"> <p> Complete results from TAREAN analysis can by downloaded as zip archive which contains the following files and directories: </p> <div class="org-src-container"> <pre class="src src-files">. . ├── clusters_info.csv <------------ list of clusters in tab delimited format ├── index.html <------------ main html report ├── seqclust │ ├── assembly # not implemented yet │ ├── blastn <------------ results of read comparison with DNA database │ ├── blastx <------------ results of read comparison with protein database │ ├── clustering │ │ ├── clusters │ │ │ ├── dir_CL0001 <----┐- detailed information about clusters │ │ │ ├── dir_CL0002 <----│ │ │ │ ├── dir_CL0003 <----│ │ │ │ .... <----┘ │ │ │ │ │ └── hitsort.cls <--------- list of reads in individual clusters │ ├── mgblast │ ├── prerun │ └── sequences <--------- input reads ├── summary # not implemented yet ├── TR_consensus_rank_1_.fasta <-- reconstructed monomer sequences for HIGH confidence satellites ├── TR_consensus_rank_2_.fasta <-- reconstructed monomer sequences for LOW confidence satellites ├── TR_consensus_rank_3_.fasta <-- reconstructed sequences of potential LTR elements └── TR_consensus_rank_4_.fasta <-- reconstructed consensus for rDNA </pre> </div> <p> List of all clusters which is available in HTML file <code>index.html</code> is also available in tab delimited format in the file <code>clusters_info.csv</code> which can be easily viewed and edited in spreadsheet editing programs. List of all clusters and the corresponding reads is in the file <code>hitsort.cls</code> which has the following format: </p> <pre class="example"> >CL1 11 134234r 55494f 85525f 136746r 96742f 91926f 239729r 105445f 222518r 136402r 9013 >CL2 10 76205r 120735r 69527r 12235r 176778f 189307f 131952f 163507f 100038r 178475r >CL3 6 99835r 222598f 29715r 102023f 99524r 30116f >CL4 6 51723r 69073r 218774r 146425f 136314r 41744f >CL5 5 70686f 65565f 234078r 50430r 68247r </pre> <p> where <code>CL1 11</code> is the cluster ID followed by number of reads in the cluster; next line contains list of all read names belonging to the cluster. </p> </div> <div id="outline-container-orgheadline6" class="outline-3"> <h3 id="orgheadline6"><span class="section-number-3">4.1</span> structure of cluster directories</h3> <div class="outline-text-3" id="text-4-1"> <p> Detailed information for each cluster is stored is subdirectories: </p> <div class="org-src-container"> <pre class="src src-folder">dir_CL0011 ├── blast.csv <------------tab delimited file, all-to-all comparison od reads within cluster ├── CL11_directed_graph.RData <----directed graph representation of cluster saved as R igraph object ├── CL11.GL <-----------------undirected graph representation of cluster saved as R igraph object ├── CL11.png <-----------┐- images with graph visualization ├── CL11_tmb.png <-----------┘ ├── dna_database_annotation.csv <-- annotation of cluster reads based on the DNA database of repeats ├── reads_all.fas <---------------- all reads included in the cluster in fasta format ├── reads.fas <---------------- subset of reads used for monomer reconstruction ├── reads_oriented.fas <------------ subset of reads all in the same orientation └── tarean ├── consensus.fasta <----------- fasta file with tandem repeat consensus variants ├── ggmin.RData ├── img │ ├── graph_11mer_1.png <-----┐ │ ├── graph_11mer_2.png <-----│ │ ├── graph_15mer_2.png <-----│ │ ├── graph_15mer_3.png <-----│ │ ├── graph_15mer_4.png <-----│ images of kmer-based graphs used for reconstruction of │ ├── graph_19mer_2.png <-----│ monomer variants │ ├── graph_19mer_4.png <-----│ │ ├── graph_19mer_5.png <-----│ │ ├── graph_23mer_2.png <-----│ │ ├── graph_27mer_3.png <-----┘ │ │ │ ├── logo_11mer_1.png <-----┐ │ ├── logo_11mer_2.png <-----│ │ ├── logo_15mer_2.png <-----│ │ ├── logo_15mer_3.png <-----│ │ ├── logo_15mer_4.png <-----│ images with DNA logos representing consensus sequences │ ├── logo_19mer_2.png <-----│ of monomer variants │ ├── logo_19mer_4.png <-----│ │ ├── logo_19mer_5.png <-----│ │ ├── logo_23mer_2.png <-----│ │ └── logo_27mer_3.png <-----┘ │ ├── ppm_11mer_1.csv <-----┐ ├── ppm_11mer_2.csv <-----│ ├── ppm_15mer_2.csv <-----│ ├── ppm_15mer_3.csv <-----│ ├── ppm_15mer_4.csv <-----│ position probability matrices for individual monomer ├── ppm_19mer_2.csv <-----│ variants derived from k-mer frequencies ├── ppm_19mer_4.csv <-----│ ├── ppm_19mer_5.csv <-----│ ├── ppm_23mer_2.csv <-----│ ├── ppm_27mer_3.csv <-----┘ │ ├── reads_oriented.fas_11.kmers <-----┐ ├── reads_oriented.fas_15.kmers <-----│ ├── reads_oriented.fas_19.kmers <-----│ k-mer frequencies calculated on oriented reads ├── reads_oriented.fas_23.kmers <-----│ for k-mer lengths 11 - 27 ├── reads_oriented.fas_27.kmers <-----┘ ├── reads_oriented.fasblast_out.cvs <---------┐results of blastn search against database of tRNA ├── reads_oriented.fasblast_out.cvs_L.csv <----│for purposes of LTR detection ├── reads_oriented.fasblast_out.cvs_R.csv <----┘ └── report.html <--- cluster analysisHTML summary </pre> </div> </div> </div> </div> </div> <div id="postamble" class="status"> <p class="author">Author: petr</p> <p class="date">Created: 2016-10-21 Pá 11:06</p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> </div> </body> </html>