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if in doubt. You have now posed this question to the list three times. The question is unclear and needs considerable refinement, IMHO. The coverage and slice functions in IRanges package are clearly relevant, and the vignette of the chipseq package illustrates their use. On Sat, Apr 3, 2010 at 8:21 PM, Kunbin Qu <[email protected]> wrote: > > Hi, > > I have run RNA-seq on 4 human samples, and I'd like to look at the count > number from each sample at regions where any of the sample has some read > coverage (say, threshold of 5 reads). What is the best way to do this? > It is basically to examine the differentially expression regions across > the transcriptome, not just limited to known annotated regions. I having > been trying to use IRanges and related packages, but things start to get > hairy when come to cluster the reads, condense them (within certain bp > range), back-track the identities. I also looked at Cufflink, but it > does not seem to be for this purpose, isn't it? Any advice is highly > appreciated. > > -Kunbin > > ______________________________________________________________________ > The contents of this electronic message, including any attachments, are > intended only for the use of the individual or entity to which they are > addressed and may contain confidential information. If you are not the > intended recipient, you are hereby notified that any use, dissemination, > distribution, or copying of this message or any attachment is strictly > prohibited. If you have received this transmission in error, please send an > e-mail to [email protected] and delete this message, along with > any attachments, from your computer. > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
