Is it correct if we use htseq counts as raw read counts in DESEq2?
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2.9 years ago

Dear all,

I am trying to get the list of differential expressed genes between two groups of HtseqCounts using DESeq2.

Now my question is if it is correct that I treat my htseq count files as raw read count files. I have previously applied Deseq2 on raw read counts and got results, so it is more straight forward to me.

I am looking forward your comments

Nazanin

RNA-Seq DESeq2 htseqCounts • 1.3k views
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What do you mean by raw counts ? Usually the counts of HTseq counts are considered raw counts and are fine to use in DESeq2.

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In this DESeq2 tutorial :

"Analyzing RNA-seq data with DESeq2 Michael I. Love, Simon Anders, and Wolfgang Huber 05/15/2018"

two different procedures has been suggested for using raw read counts and htseqCounts in DESeq2 and I wander to know if it is OK to use htseq counts with the commands suggested for raw read counts

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In this context, "raw counts" refers to unnormalized integer-only counts of reads/fragments uniquely mapping to genes.

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2.9 years ago

Yes, the count files produced by htseq-count are appropriate input into DESeq2.

BTW, featureCounts is much faster.

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Thank you so much for your help

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