Question: Is it correct if we use htseq counts as raw read counts in DESEq2?
0
gravatar for nazaninhoseinkhan
3 months ago by
Iran, Islamic Republic Of
nazaninhoseinkhan270 wrote:

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 • 152 views
ADD COMMENTlink modified 3 months ago by Devon Ryan84k • written 3 months ago by nazaninhoseinkhan270

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

ADD REPLYlink written 3 months ago by Carlo Yague4.3k

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

ADD REPLYlink written 3 months ago by nazaninhoseinkhan270

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

ADD REPLYlink written 3 months ago by Devon Ryan84k
2
gravatar for Devon Ryan
3 months ago by
Devon Ryan84k
Freiburg, Germany
Devon Ryan84k wrote:

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

BTW, featureCounts is much faster.

ADD COMMENTlink modified 3 months ago • written 3 months ago by Devon Ryan84k

Thank you so much for your help

ADD REPLYlink written 3 months ago by nazaninhoseinkhan270
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