8c520f540bf2410ce30bbf71f16f292b90144a5a Merge parents cd059ca 11bfdf3 dschmelt Wed Sep 7 14:06:50 2022 -0700 Fixing merge, going with markD's changes refs #29356 diff --cc src/hg/htdocs/goldenPath/help/bigRmsk.html index ab2bf64,72eac77..839b9ea --- src/hg/htdocs/goldenPath/help/bigRmsk.html +++ src/hg/htdocs/goldenPath/help/bigRmsk.html @@@ -1,79 -1,70 +1,73 @@@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser bigRmsk RepeatMasker Format" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>bigRmsk Track Format</h1> <p> The bigRmsk format allows for the display of annotations of a genome generated by the <a href="http://www.repeatmasker.org/" target="_blank">RepeatMasker</a> program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. + It is the recommend method of adding RepeatMaster tracks to assembly hubs. + For a descriptions of this features of this track type, with examples, see + <a href="bigRmskTrackDescExample.html">standard bigRmsk track description</a>. + <p> The bigRmsk format enables taking the annotation output of RepeatMasker and converting it into a compressed and indexed <a href="/goldenPath/help/bigBed.html">bigBed</a> file. Please see this page for a details of the bigBed format, its use, and associated tools. </p> <h2 id="bigRmsk">bigRmsk track definitions</h2> <p> The bigRmsk tracks consist of two bigBed files define by <a href="http://www.linuxjournal.com/article/5949" target="_blank">autoSql</a> schema: </p> <ul> - <li>The primary bigRmsk file, define by <a href="examples/bigRmskBed.as"><em>bigRmskBed.as</em></a>, + <li>The primary bigRmsk file, define by <a href="examples/bigRmskBed.as"> + <em>bigRmskBed.as</em></a>, which has the annotations of repeats. - <li>The secondary bigRmskAlign file, define by <a href="examples/bigRmskAlignBed.as"><em>bigRmskAlignBed.as</em></a>, - which contains the alignments of the consensus repeats to the genome. This file is optional, if omitted, - the bigRmsk track will function, without the ability to view the alignments. + <li>The secondary bigRmskAlign file, define by <a href="examples/bigRmskAlignBed.as"> + <em>bigRmskAlignBed.as</em></a>, + which contains the alignments of the consensus repeats to the genome. This file is optional, + if omitted, the bigRmsk track will function, without the ability to view the alignments. </ul> <p> - The input files for the bigRmsk files are create from the RepeatMasker <em>*.out</em> and <em>*.align</em> files - using the <em>rmToTrackHub.pl</em> program that is include with RepeatMasker. The bigRmsk + The input files for the bigRmsk files are created from the RepeatMasker <em>*.out</em> and + <em>*.align</em> files + using the <em>rmToTrackHub.pl</em> program that is included with RepeatMasker. The bigRmsk format is not designed to work with any other type of data. </p> <h2 id="steps">Creating a bigRmsk track</h2> <p> - To create a bigRmsk track, and its supporting files, follow the below steps. + To create a bigRmsk track and its supporting files, follow the below steps. This assumes that you have already run RepeatMasker and have a <em>*.out</em>, and optionally <em>*.align</em> file. </p> <p> - RepeatMasker output files are converted to the bigRmsk textual form using the - <em>RepeatMasker/util/rmToTrackHub.pl</em> program that is part of the RepeatMasker distribution. - </p> - <p> - NOTE: The April 2021 version of RepeatMasker (4.1.2-p1) does not contain the - <em>rmToTrackHub.pl</em> program. Until it is included, obtain a copy - from the RepeatMasker GitHub development branch: + RepeatMasker output files are convert to the bigRmsk textual form using the + <em>RepeatMasker/util/rmToTrackHub.pl</em> program that is part of the + <a href="http://www.repeatmasker.org/RepeatMasker/">RepeatMasker 4.1.3 or newer distribution</a>. </p> - <pre> - <code> - git clone -b development git@github.com:rmhubley/RepeatMasker.git - </code> - </pre> - <p> <strong>Step 1.</strong> If you wish to experiment with quickly building an example track, download the example RepeatMasker output files for the human GRCh38 (hg38) assembly <a href="examples/bigRmskExample.out">bigRmskExample.out</a> and <a href="examples/bigRmskExample.align">bigRmskExample.align</a> used in this tutorial: <pre> <code> wget https://genome.ucsc.edu/goldenPath/help/examples/bigRmskExample.out wget https://genome.ucsc.edu/goldenPath/help/examples/bigRmskExample.align </code> </pre> <p> Otherwise, substitute your <em>*.out</em> and <em>*.align</em> in theses instructions.