[Bioc-sig-seq] counts differences among multiple RNA-seq samples

[Nicolas Delhomme]

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: nicolas.delhomme at embl.de
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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