Entering edit mode
5.8 years ago
nazaninhoseinkhan
▴
520
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
What do you mean by raw counts ? Usually the counts of HTseq counts are considered raw counts and are fine to use in DESeq2.
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
In this context, "raw counts" refers to unnormalized integer-only counts of reads/fragments uniquely mapping to genes.