Hi

It is true that HTSeq from python and easyRNASeq give different counts using the same annotation file (gtf from ensembl). This was for
Dmelanogaster. The bam file used to get count tables were from tophat/bowtie.


easyRNASeq:
> head(countTable)
              accepted_hits.bam
"FBgn0000003"              1632
"FBgn0000008"              1156
"FBgn0000014"               198
"FBgn0000015"               129
"FBgn0000017"              5270
"FBgn0000018"               616

HTSeq:
FBgn0000003    0
FBgn0000008    1229
FBgn0000014    206
FBgn0000015    137
FBgn0000017    5508
FBgn0000018    631

Nicco directed me to previous posts where someone had studied this. If you are interested, google "counting RNA-seq reads in R/BioC" (with quotes) to find the posts.

Silav



________________________________
 From: Steve Lianoglou <mailinglist.honeypot@gmail.com>
To: Fatemehsadat Seyednasrollah <fatsey@utu.fi> 
Cc: "bioconductor@r-project.org" <bioconductor@r-project.org> 
Sent: Friday, December 14, 2012 10:13 AM
Subject: Re: [BioC] Different number of genes when using HTseq and cuffdiff

On Fri, Dec 14, 2012 at 9:51 AM, Fatemehsadat Seyednasrollah
<fatsey@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@gmail.com]
> Sent: Friday, December 14, 2012 4:49 PM
> To: Fatemehsadat Seyednasrollah
> Cc: bioconductor@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@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

_______________________________________________
Bioconductor mailing list
Bioconductor@r-project.org
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
	[[alternative HTML version deleted]]

