Hello Medhi,

Sorry for the slow reply.

It's not clear from your question, but let's assume that you have 3 lanes of 
RNA-seq data for each of your samples. In this case, here's a reasonable 
approach for analyzing this data:

(1) Run Tophat + Cufflinks on each lane of data;
(2) Use Cuffcompare on *all* transcripts produced by Cufflinks for all data;
(3) Run Cuffdiff using (a) the combined transcripts produced by Cuffcompare and 
(b) segmenting the mapped reads produced by Tophat into groups based on the 
sample that they came from.

Let us know if you have more questions.


On Feb 1, 2011, at 8:54 AM, Motallebipour, Mehdi wrote:

> Hi,
> I am trying to analyze some RNA-seq data using the Galaxy. The reads for each 
> sample comes from 3 lanes, so I need to integrate these three lane reads to 
> be able to make a comparison between my samples. How do I 'put together' 
> these three read-files? Is there any tools available in Galaxy for that, 
> which I have missed? Unfortunately I do not have any programming skills.
> Many thanks,
> Mehdi M
> ----------------------------------------
> Mehdi Motallebipour, PhD
> Mammalian Neurogenesis
> MRC Clinical Sciences Centre
> Imperial College London
> Hammersmith Hospital Campus
> Du Cane Road
> London
> W12 0NN
> United Kingdom
> Tel: +44-20-8383 8285
> _______________________________________________
> galaxy-user mailing list
> galaxy-user@lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-user

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