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

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
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updated by Devon Ryan Devon Ryan • written by syrez • syrez

1 answer

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.

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written by Devon Ryan Devon Ryan

Hi Devon!

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

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written by syrez • syrez

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