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

[Steve Lianoglou]

On Fri, Dec 14, 2012 at 9:51 AM, Fatemehsadat Seyednasrollah
<fatsey at utu.fi> wrote:
> 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.

This is hard to debug blind -- have you tried looking at the genes +
your data in something like IGV to see if you can figure this out?

Does this have something to do w/ how each tool handles "overlapping" regions?

Are there multimap reads that these tools handle differently? Are they
they filtering reads differently based on alignment quality, maybe?

Lots of things to check.

-steve

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



-- 
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