Import Salmon outputs into DESeq2

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

into outputs deseq2 import tximport using salmon

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written 4.6 years ago by kimmitzka •

1 answer

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.

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written 4.6 years ago by noorpratap.singh

Alternativey, tximport which is a bit more lightweight.

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written 4.6 years ago by ATpoint

I see, thx

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written 4.6 years ago by kimmitzka •

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