Hi all,
Has anyone here used refgenie before to obtain genome indices? I have used it recently for Salmon:
When viewing the asset_parents for this, it lists the following fasta transcriptome:
Which based on the IDs is obtained from Ensembl, however I don't seem to have a way to view the Ensembl version used? I need to know this to obtain the matching version gtf annotation for some other work I'm doing.
If anyone who has used refgenie is able to lend some words of wisdom would be much appreciated.
Thanks,
Nick
•
written
by
nick_b55 •
This seems to be the matching GTF: http://refgenomes.databio.org/v3/assets/splash/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/ensembl_gtf?tag=default
That's brilliant, yes I see the code for that GTF matches the fasta used to build the salmon index.
Many thanks for your help, I wouldn't have found that without it!
Log in to answer this question.
