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.