Import Salmon outputs into DESeq2

Question

[kimmitzka]

Hi all,

I want to import salmon transcript estimate output fiels into DESeq2 using tximport. But I have a question. The output of salmon is in TPM But the DESeq2 needs raw data. Is my understanding right or not？

Sincerely, Kimi

Answer 1

[noorpratap.singh]

The vignette here provides a detailed description of how to import salmon counts. You are right DESeq2 requires raw counts and numReads in quant.sf for Salmon run provides that.

[ATpoint]

Alternativey, tximport which is a bit more lightweight.

[kimmitzka]

I see, thx