Hello David,

Given the data size, using a local instance is your best option right now. Fairly soon, using the cloud would also work (as long as the analysis keeps total size under the 1TB). There are a few issues that prevent us from recommending the cloud right now, but we are actively working to bring functionality up to full speed, so feel free to check back soon (~ few weeks) if you'd like an update.

Best wishes for your project,

Galaxy team

On 1/31/11 12:33 PM, Martin, David A. wrote:

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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