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

[Steve Lianoglou]

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
Contact Info: http://cbio.mskcc.org/~lianos/contact