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

Question

[nazaninhoseinkhan]

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

[Carlo Yague]

What do you mean by raw counts ? Usually the counts of HTseq counts are considered raw counts and are fine to use in DESeq2.

[nazaninhoseinkhan]

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

[Devon Ryan]

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

Answer 1

[Devon Ryan]

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

BTW, featureCounts is much faster.

[nazaninhoseinkhan]

Thank you so much for your help