[BioC] question about DeSeq

Martin Morgan mtmorgan at fhcrc.org
Wed Dec 22 14:57:39 CET 2010

On 12/22/2010 05:24 AM, Simon Anders wrote:
> Hi
> On 12/22/2010 08:23 AM, vasu punj wrote:
>> What kind of input DEseq can take Can it take Cufflinks out put or we
>> have to use FKPM conversion.
> DESeq needs integer counts, i.e., just the raw number of reads that
> align to a feature, without any normalization for sequencing depth or
> transcript length. Hence, the FPKM values reported by cufflinks are not
> suitable. the easiest is to use HTSeq-count to get a table of raw counts.
> http://www-huber.embl.de/users/anders/HTSeq/
> http://www-huber.embl.de/users/anders/HTSeq/doc/count.html

It is as straight-forward and flexible to count overlaps with
Bioconductor IRanges countOverlaps, with the added advantages of
integration with annotation resources (e.g., GenomicFeatures
TranscriptDb) and familiar (to those on the Bioconductor mailing list)
programming environment.


>   Simon
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