Question

Import Salmon outputs into DESeq2

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2.9 years ago

kimmitzka • 0

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 • 3.6k views

ADD COMMENT • link 2.9 years ago by kimmitzka • 0

score 1 · Answer 1 · 2022-01-03

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2.9 years ago

noorpratap.singh ▴ 330

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.

ADD COMMENT • link 2.9 years ago by noorpratap.singh ▴ 330

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Alternativey, tximport which is a bit more lightweight.

ADD REPLY • link 2.9 years ago by ATpoint 85k

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I see, thx

ADD REPLY • link 2.9 years ago by kimmitzka • 0