Import Salmon outputs into DESeq2
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4 months 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´╝č

Sincerely, Kimi

into outputs DESeq2 Import tximport using Salmon • 678 views
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4 months ago

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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Alternativey, tximport which is a bit more lightweight.

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I see, thx

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