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? I will appreciate your help Alejandro -- output of sessionInfo(): - -- Sent via the guest posting facility at bioconductor.org.

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(): > > - > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]