Where is the IGV hg38 gene track from

Question

[alex.v.nesta]

This is a simple question, but I can't find the question anywhere.

See photo. When I load the hg19 genome it says Refseq Genes. When I load hg38 it just says genes. What does this mean?

I'm mainly concerned because it contains more information than gencode v28, so I need to know where the information is coming from and if it's reliable.

[jockbanan]

Hi! I also thought so, but I just found some discrepancies. One example is MYC:

in the current RefGene track, transcript NM_002467 has transcription end at: 127742951

In the current IGV track, transcript NM_002467 has transcription end at: 127741434

I also checked an older (August 2018) version of of RefGene and it contains the same transcription end as the current one, so nor that version is concordant with the IGV track. I still wonder where that IGV track comes from.

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question.

Consider reporting this directly to IGV developers. Jim Robinson is author of IGV but has not logged in to biostars for some months.

Answer 1

[Jim Robinson]

Hi, from UCSC, its the UCSC Refseq track. Specifically http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz