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

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Thu Apr 15 17:43:56 CEST 2010


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 <delhomme at embl.de> 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: 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
>>
>>
>>
>>
>> ______________________________________________________________________
>> 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 postmaster at genomichealth.com and delete this message, along with
>> any attachments, from your computer.
>>
>> _______________________________________________
>> Bioc-sig-sequencing mailing list
>> Bioc-sig-sequencing at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>



More information about the Bioc-sig-sequencing mailing list