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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 <KQu@genomichealth.com> 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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