From transcripts counts of Salmon to genes counts needed by edgeR

Question

[Sharon]

I am new to using edgeR and Salmon. I have transcripts counts from Salmon. However I Realized that edgeR starts with genes counts. As far as I know Salmon and edgeR are used together a lot. So my question is how can I convert my transcripts counts to genes counts to proceed with edgeR? Or am I missing something? Like this is not what we should do. Thanks

Answer 1

[Devon Ryan]

You can use the tximport package, which is available in bioconductor.

Answer 2

[Rob]

The package tximport provides an easy way to aggregate transcript level abundances to gene-level counts, and is likely the most popular approach in this kind of pipeline. edit: looks like Devon beat me to it by a few seconds ;P.