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 @@ File Format page include a "track type=..." 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 bedToBigBed or validateFiles, outside of the Browser. To see an example of using bedToBigBed with correct input data types, follow this link. More information about track lines can be found here.

Non-UCSC style chromosome names

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')?

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 Assembly Gateway page or as a "chromAlias.txt" file from our downloads server under the link "Genome sequence files and select annotations" for that assembly.