GFF/GTF file download from UCSC or gnomAD

Question

[storm1907]

Hello, I need to download GFF/GTF file from somewhere, preferably UCSC or gnomAD; I have never done that - can somebody instruct, how to download them correctly?

Thank you!

Answer 1

[Juke34]

For human: Go there http://hgdownload.soe.ucsc.edu/goldenPath/archive/hg38/ncbiRefSeq/ and click on it.

Otherwise copy the link and run a wget in a terminal like this

wget http://hgdownload.soe.ucsc.edu/goldenPath/archive/hg38/ncbiRefSeq/hg38.2021-02-10.ncbiRefSeq.gtf.gz

I would suggest to download the file directly from Refseq raher than UCSC that will at some point mirror few files from there:

https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/