822194a76aaec283cb1699653d5ad3433c7e44ba mspeir Thu Apr 24 16:20:58 2025 -0700 adding FAQ entry about special characters in labels, adding links to that FAQ to short/longLabel entries in trackDbDoc, and fixing minor formatting error with maxWindowCoverage section, refs #35003 diff --git src/hg/htdocs/FAQ/FAQcustom.html src/hg/htdocs/FAQ/FAQcustom.html index 6bcf1c18187..f10d4d45652 100755 --- src/hg/htdocs/FAQ/FAQcustom.html +++ src/hg/htdocs/FAQ/FAQcustom.html @@ -10,30 +10,31 @@ <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 <li><a href="#custom12">Non-UCSC chromosome names</a></li> +<li><a href="#custom13">Apostrophes and special characters in track labels</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>, @@ -165,17 +166,27 @@ <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 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. +<a name="custom13"></a> +<h2>Apostrophes and special characters in track labels</h2> +<h6>How can I put an apostrophe in my track label?</h6> +<p> +The Genome Browser supports a limited set of characters in the track image. In +addition to the characters <code>a-z</code> and <code>A-Z</code>, it supports +some accented characters such as <code>é</code> or <code>á</code> and apostrophes, +specifically "<code>ʹ</code>" (which corresponds to Unicode character U+2019). +If there are characters in your track's short or long label that we don't +currently support, <a href="../contacts.html">contact us</a>. <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->