[BioC] package to count read prior to DESeq?

Abhishek Pratap apratap at lbl.gov
Fri Feb 3 19:51:32 CET 2012


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
>
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> ---------------------------------------------------------------
>
>
>
>
>
> 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
>>
>>
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