Question: File containing a mapping of transcripts to genes - Salmon on Galaxy
0
gravatar for syrez
3.6 years ago by
syrez40
Chicago
syrez40 wrote:

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

rna-seq salmon galaxy • 1.7k views
ADD COMMENTlink modified 3.6 years ago by Devon Ryan97k • written 3.6 years ago by syrez40
2
gravatar for Devon Ryan
3.6 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

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.

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Devon Ryan97k

Hi Devon!

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

ADD REPLYlink written 3.6 years ago by syrez40

Weird, anyway:

  1. Go to Ensembl biomart
  2. Select mouse
  3. Select "get results" and then "go".
ADD REPLYlink written 3.6 years ago by Devon Ryan97k
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