Refgenie - salmon_sa_index Ensembl version

Question

[nick_b55]

Hi all,

Has anyone here used refgenie before to obtain genome indices? I have used it recently for Salmon:

http://refgenomes.databio.org/v3/assets/splash/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/salmon_sa_index?tag=default

When viewing the asset_parents for this, it lists the following fasta transcriptome:

http://refgenomes.databio.org/v3/assets/splash/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/fasta_txome?tag=default

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

Answer 1

[GenoMax]

This seems to be the matching GTF: http://refgenomes.databio.org/v3/assets/splash/2230c535660fb4774114bfa966a62f823fdb6d21acf138d4/ensembl_gtf?tag=default

[nick_b55]

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!