[BioC] Different number of genes when using HTseq and cuffdiff

[Fatemehsadat Seyednasrollah]

Hi,

By more genes I do not mean number of DE genes but the number of total input genes.
I have used the same tophat bam files as the input of HTSeq and cuffdiff but in the results regardless of how many DE genes I have, there are different number of total genes.
And yes I am using the latest version of both(cuffdiff2)

Thanks in advance
________________________________________
From: Steve Lianoglou [mailinglist.honeypot at gmail.com]
Sent: Friday, December 14, 2012 4:41 PM
To: Fatemehsadat Seyednasrollah
Cc: bioconductor at r-project.org
Subject: Re: [BioC] Different number of genes when using HTseq and cuffdiff

Hi,

On Fri, Dec 14, 2012 at 9:05 AM, Fatemehsadat Seyednasrollah
<fatsey at utu.fi> wrote:
> Hi,
>
>  I have used the same output tophat bam files both for HTseq (and then DESeq) and cuffdiff to find DE genes. But  I do not understand why even when the bam files and references are the same the number of genes are different in the result of cuffdiff and HTseq. Actually I expected to have different number of counts for each gene but not getting more (nearly 100) number of genes in HTseq comparing to cuffdiff.

What do you mean by "more genes"? You mean more genes are called as
differentially expressed? Or is there some pipeline that you are using
to just count reads over genes, and these two pipelines are giving
different number of genes as "input"?

If it's the former -- cuffdiff and DESeq do rather different things to
assess differential expression, and so your result should not be a
surprise.

While I haven't actually read the paper, I would imagine the new
publication on cuffdiff2 would be rather informative in this regard:

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2450.html

You haven't said what version of each software you are using, but I
guess you're using cuffdiff 2?

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact