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
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