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.

Thanks,
J.

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