[BioC] package to count read prior to DESeq?

[Abhishek Pratap]

Hi Nico

With respect to easyRNAeq package I am wondering if I supply it a
transcript level gtf file can it produce gene level counts. Basically
the file is the output from cufflinks.

the last(attributes) column in the file does have the gene_id attribute.


Best,
-Abhi



On Fri, Feb 3, 2012 at 8:06 AM, Nicolas Delhomme <delhomme at embl.de> wrote:
> Hi Nat,
>
> That's what the easyRNASeq (Bioc 2.10) pacakge exactly is for. Let me know if you need any help.
>
> Cheers,
>
> Nico
>
> ---------------------------------------------------------------
> Nicolas Delhomme
>
> Genome Biology Computational Support
>
> European Molecular Biology Laboratory
>
> Tel: +49 6221 387 8310
> Email: nicolas.delhomme at embl.de
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
> ---------------------------------------------------------------
>
>
>
>
>
> On 3 Feb 2012, at 16:39, nathalie wrote:
>
>> Hi,
>> Is there a package to create a count table from bam files, which gives an output compatible with DESeq analysis?
>> thanks
>> Nat
>>
>>
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor