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| author | petr-novak |
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| date | Thu, 19 Dec 2019 10:24:45 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/tarean_output_help.html Thu Dec 19 10:24:45 2019 -0500 @@ -0,0 +1,399 @@ +<?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>