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

[Fatemehsadat Seyednasrollah]

I am using the same gtf file for both. Actually this is why I do not understand this variation between them.
I was thinking maybe cuffidff may discard some genes with very low number of counts but I did not find something which support this idea.

________________________________________
From: Steve Lianoglou [mailinglist.honeypot at gmail.com]
Sent: Friday, December 14, 2012 4:49 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 9:45 AM, Fatemehsadat Seyednasrollah
<fatsey at utu.fi> wrote:
> 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)

So, isn't this a function of the gene annotation files (gft's) you are
using for each tool?

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
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