[BioC] question about DeSeq

[Simon Anders]

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

   Simon