If you are mainly interested in counting, you should check out Genominator which has been capable of doing this for a large number of samples for a long time. It should be fairly easy to use, with the biggest huddle usually being reading in the data at first.
Kasper On Thu, Apr 15, 2010 at 11:23 AM, Nicolas Delhomme <[email protected]> wrote: > Hi Kunbin, > > I'm currently developing an R package that does something close to what you > describe. Maybe we can discuss more in details what you need, off list, to > see if I can help you out? If it turns out to be the case, then we'll post > back the result to the list. > > Cheers, > > --------------------------------------------------------------- > Nicolas Delhomme > > High Throughput Functional Genomics Center > > European Molecular Biology Laboratory > > Tel: +49 6221 387 8310 > Email: [email protected] > Meyerhofstrasse 1 - Postfach 10.2209 > 69102 Heidelberg, Germany > --------------------------------------------------------------- > > > > > On 3 Apr 2010, at 05:48, Kunbin Qu 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 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
