Thanks Simon for the link. It does answer my question. FYI, I am using HTSeq.scripts.count in HTSeq. Regards, Nirmala -----Original Message----- From: Simon Anders [mailto:anders@embl.de] Sent: Thursday, July 19, 2012 3:52 PM To: bioconductor at r-project.org Subject: Re: [BioC] counts from HTSeq vs DEXSeq Hi > I used HTSeq to count the reads in RNA-seq data. When I used these > counts in DEXSeq and execute the function geneCountTable, the counts > generated from geneCountTable are different compared to the original > HTSeq counts. Did anyone observe this discrepancy? I'm not sure if In understand your question. Which HTSeq script have you used? See also this thread, which might answer your question: http://seqanswers.com/forums/showthread.php?t=15637 Simon _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor