hi Alejandro


On Mon, Aug 26, 2013 at 10:28 PM, Alejandro [guest] <guest@bioconductor.org>
wrote:
>
>
> DESeq needs count data in the form of rectangular table. My question is
whether is correct or possible to use the genes.count_tracking file
generated with cuffdiff as the  counts table that DESeq requires?


​Scanning
 the
​ information in
 the cuff
​diff​
manual
​...​


"Primary transcript and gene counts are computed by summing the counts of
transcripts in each primary transcript group or gene group.
...
genes.count_tracking
Gene counts. Tracks the summed counts of transcripts sharing each gene_id
"
http://cufflinks.cbcb.umd.edu/manual.html

​this sounds like you will end up with a read counted multiple times, if
the read can align to multiple transcripts.

T
​he counting method we recommend (as produced by htseq-count or
summarizeOverlaps), counts a read only once.

For more on this you can search the mailing list for 'deseq double count',
e.g.:

https://stat.ethz.ch/pipermail/bioconductor/2012-April/044717.html

​​

​Mike​



>
>
> I will appreciate your help
> Alejandro
>
>  -- output of sessionInfo():
>
> -
>
> --
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