dcb079b13428b8d0416d44ec2626482fab2f3e53 mspeir Wed Jan 15 15:23:45 2025 -0800 minor corrections based on code review, refs #35025 diff --git src/hg/htdocs/FAQ/FAQcustom.html src/hg/htdocs/FAQ/FAQcustom.html index 2b96316..6bcf1c1 100755 --- src/hg/htdocs/FAQ/FAQcustom.html +++ src/hg/htdocs/FAQ/FAQcustom.html @@ -155,27 +155,27 @@ <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' +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 +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. <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->