edb12b1895c6b72181ad7020eee9a6d52e49df74 mspeir Sun Jan 5 14:09:00 2025 -0800 Adding details about chromAlias stuff to various custom track pages, refs #26360 diff --git src/hg/htdocs/FAQ/FAQcustom.html src/hg/htdocs/FAQ/FAQcustom.html index e9ae0b6..2b96316 100755 --- src/hg/htdocs/FAQ/FAQcustom.html +++ src/hg/htdocs/FAQ/FAQcustom.html @@ -9,31 +9,31 @@ <h2>Topics</h2> <ul> <li><a href="#custom1">Displaying personal annotation data in the Genome Browser</a></li> <li><a href="#custom2">Adding a personal annotation track to the Genome Browser website</a></li> <li><a href="#custom3">Defining filter parameters for custom tracks</a></li> <li><a href="#custom4">Coloring a custom track using the useScore parameter</a></li> <li><a href="#custom5">Constructing a Genome Browser URL</a></li> <li><a href="#custom6">Using the hgsid parameter in a URL</a></li> <li><a href="#custom7">Creating a details page for a custom annotation track</a></li> <li><a href="#custom8">Custom annotation track troubleshooting</a></li> <li><a href="#custom9">Error 500: Internal server error</a></li> <li><a href="#custom10">Byte-range request error</a></li> <li><a href="#custom11">BedToBigBed and other utilities fail because of custom track header -lines</a></li> +<li><a href="#custom12">Non-UCSC chromosome names</a></li> </ul> <hr> <p> <a href="index.html">Return to FAQ Table of Contents</a> </p> <a name="custom1"></a> <h2>Displaying personal annotation data in the Genome Browser</h2> <p> <h6>How do I display my own personal annotation data in the Genome Browser?</h6> <p> To create an annotation track that will display on the Genome Browser, you must first organize your data into a format supported by the browser custom track feature: <a href="FAQformat.html#format4">GTF</a>, <a href="FAQformat.html#format3">GFF</a>, <a href="FAQformat.html#format1">BED</a>, @@ -148,16 +148,34 @@ <a name="custom11"></a> <h2>BedToBigBed and other utilities fail because of custom track header lines</h2> <h6>Why does my custom track fail when I use <code>bedToBigBed</code> or utilities like <code>validateFiles</code>?</h6> <p> These utilities can fail when the input includes custom-track-specific lines at the top of the file that are not considered part of the data. Many of the custom track examples on the <a href="FAQformat.html" target="_blank">File Format</a> page include a "<code>track type=...</code>" line that is specific for loading the data into the Browser. This line will cause raw data files to fail validation by other tools, such as <code>bedToBigBed</code> or <code>validateFiles</code>, outside of the Browser. To see an example of using <code>bedToBigBed</code> with correct input data types, follow this <a href="../goldenPath/help/bigBed.html#Ex3" target="_blank">link</a>. More information about track lines can be found <a href="../goldenPath/help/customTrack.html#TRACK" target="_blank">here</a>.</p> +<a name="custom12"></a> +<h2>Non-UCSC style chromosome names</h2> +<h6>Can I upload a custom track with chromosome names (e.g. '1' or 'NC_000001.11') that don't +match the UCSC-style chromosome names (e.g. 'chr1', 'chrX')?</h6> +<p> +As of 2018, you can upload a custom track that contains either +UCSC-style chromosome names (e.g. 'chr1', 'chrX') or one of several supported +aliases, typically from Ensembl (e.g. '1' or 'X'), Genbank (e.g. 'CM000663.2' +or 'CM000685.2'), or RefSeq (e.g. 'NC_000001.11' or 'NC_000023.11'). Many +different custom track types support this, including BED, BAM, and any of +our big* formats like bigBed or bigWig. You can view the list of supported +aliases by clicking on the "View sequences" link for your assembly assembly of +interest from the <a href="../cgi-bin/hgGateway">Assembly Gateway page</a> or +as a "chromAlias.txt" file from <a +href="https://hgdownload.soe.ucsc.edu/downloads.html" >our downloads server</a> +under the link "Genome sequence files and select annotations" for that assembly. + + <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->