Question: Is it correct if we use htseq counts as raw read counts in DESEq2?
0
gravatar for nazaninhoseinkhan
25 days ago by
Iran, Islamic Republic Of
nazaninhoseinkhan240 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 • 87 views
ADD COMMENTlink modified 25 days ago by Devon Ryan81k • written 25 days ago by nazaninhoseinkhan240

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 25 days ago by Carlo Yague4.0k

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 25 days ago by nazaninhoseinkhan240

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

ADD REPLYlink written 25 days ago by Devon Ryan81k
2
gravatar for Devon Ryan
25 days ago by
Devon Ryan81k
Freiburg, Germany
Devon Ryan81k wrote:

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

BTW, featureCounts is much faster.

ADD COMMENTlink modified 25 days ago • written 25 days ago by Devon Ryan81k

Thank you so much for your help

ADD REPLYlink written 25 days ago by nazaninhoseinkhan240
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