I have a total 84 GB of Illumina reads (20 lanes total).  I wasn't sure if I 
could analyze this amount of data on the public server or if this would bog 
down the system.  I am looking to do a gene expression comparison between two 
groups of 10 animals using Tophat and Cufflinks.  Can anyone tell me if this is 
okay or if I must try and use the Cloud for this analysis..  I am assuming the 
FTP option is the best for uploading this data.  Thank you,

David Martin

-----Original Message-----
From: jgoe...@gmail.com on behalf of Jeremy Goecks
Sent: Fri 1/21/2011 12:41 PM
To: Rory Kirchner
Cc: Martin, David A.; galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] Galaxy for gene expression comparison
> > I have patched galaxy to have cuffdiff handle replicates and to do
> normalization, when that gets merged into the main branch your workflow will
> be the same except you won't have to merge all of the bam files from each
> condition together to use cuffdiff.

Hi all,

I merged Rory's changes into galaxy-central, so Cuffdiff now supports
replicates. I'll see what I can do for Cuffcompare; in the near-term,
repeated merging using Cuffcompare will produce a GTF file that is both
correct and usable with Cuffdiff.


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