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, Jen Galaxy team On 1/31/11 12:33 PM, Martin, David A. wrote:
Hello,
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: jgoecks@gmail.com on behalf of Jeremy Goecks Sent: Fri 1/21/2011 12:41 PM To: Rory Kirchner Cc: Martin, David A.; galaxy-user@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.
Thanks, J.
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