File containing a mapping of transcripts to genes - Salmon on Galaxy

Question

[syrez]

Hello there!

Could someone please help me download mapping of transcripts to genes that I can use with the Salmon tool on Galaxy? I tried UCSC Genome browser but I'm not sure if I'm doing the right thing.

Thanks, Manish

Answer 1

[Devon Ryan]

Here's an example query using biomart. Note that you'd need to swap the columns, but you can do that in Galaxy. If you need different gene/transcript identifiers then you can probably get them from biomart too.

BTW, there's a separate biostar site for Galaxy.

[syrez]

Hi Devon!

Thanks so much for the input. The example query link is down for some reason, maybe it's temporary.

[Devon Ryan]

Weird, anyway:

1. Go to Ensembl biomart
2. Select mouse
3. Select "get results" and then "go".