Question: From transcripts counts of Salmon to genes counts needed by edgeR
0
gravatar for Sharon
3.2 years ago by
Sharon490
Sharon490 wrote:

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

edger rna-seq salmon • 2.5k views
ADD COMMENTlink modified 3.2 years ago by Rob4.6k • written 3.2 years ago by Sharon490
2
gravatar for Devon Ryan
3.2 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

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

ADD COMMENTlink written 3.2 years ago by Devon Ryan98k
2
gravatar for Rob
3.2 years ago by
Rob4.6k
United States
Rob4.6k wrote:

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.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Rob4.6k
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