Refgenie - salmon_sa_index Ensembl version
1
1
Entering edit mode
2.2 years ago
nick_b55 ▴ 10

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

refgenie index salmon transcriptome • 907 views
ADD COMMENT
2
Entering edit mode
ADD COMMENT
0
Entering edit mode

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!

ADD REPLY

Login before adding your answer.

Traffic: 2508 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6