issue with HGNC tablebrowser output
Dominic Owens
Hi UCSC,
When I download table from table browser:
Mammal > Human > GRCh38/hg38 > Genes and Gene Predictions > HGNC > hgnc
Strand information (column 6) is all listed as “+” for all rows. There must be a mistake somewhere…
As an aside, I like the HGNC table as it includes information such as “protein coding” or “pseudogene” which is useful for filtering, but not having correct strand information is a bit difficult and I am having to merge HGNC info with another table to have both strand and this additional annotation information.
Thanks,
Dominic
Luis Nassar
Hi, Dominic.
Thank you for your patience while we looked into this.
The HGNC track's metadata comes directly from the data dump:
http://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt
Unfortunately, that file did not contain the strand information. In order to conform it to our bed formats, we had to add a few extra fields at the start one of which was strand. We made the mistake of making them all "+" instead of our usual "." placeholder value. We have now fixed this.
Could you describe what you are trying to extract? If you are looking for protein coding/pseudogene lists, we could probably suggest a better way to extract that from one of your gene annotation tracks.
I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.
Lou Nassar
UCSC Genomics Institute
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