7.9 years ago by
Bay Area, CA
Giovanni has a good answer!
Here are two more options, if you are really interested in obtaining a gene name/symbol. When obtaining a reference gene track to compare against, try one of the following:
From the RefSeq Genes track, pull in the entire regGene file over to Galaxy, not just the default BED version (output format = all fields from selected table). Once in Galaxy, delete the first column (bin). Set file type as interval. Cut/merge the columns of the file to produce a BED4 format file (chrom, start, stop, name), using c12 as the "name" attribute and Join (inner, probably) to preserve the name in the output. C12 is actually name2 == Gene name/symbol in the UCSC table description (where c1 is name == just the RefSeq ID and what would be in a simple BED file output directly from the UCSC Table Browser).
Another data option is the UCSC Genes track, which also would have to be modified a bit to obtain a gene name/symbol. To do this, select the UCSC Genes track, output format = "selected fields from primary and related tables", submit, link in from kgXref the identifier(s) of choice, submit and send to Galaxy. Set file type as interval. Cut columns/merge to create a BED4 format file, using that alternate identifier as the "name" interval attribute during the Join ("name" from a simple BED output for this track would be UCSC's internal transcript identifier).
After the Join, cut columns out to produce a simple BED file, change file type to BED, create a custom track line (or not), and display at UCSC or directly in Galaxy using Trackster ("Visualization").
Hopefully this helps,