>
> > 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 chang
> I am not sure about cuffcompare, but cuffdiff doesn't generate any extra
> files if you add more groups and replicates to the command line. It adds
> columns to the output files but the number of files remains the same.
Hmm. This is a new and welcome change.
> For a workflow for Martin for n
I am not sure about cuffcompare, but cuffdiff doesn't generate any extra files
if you add more groups and replicates to the command line. It adds columns to
the output files but the number of files remains the same.
For a workflow for Martin for now, I would suggest doing this for making calls
> Thank you for the suggestions. Ultimately, I would like to compare
> gene(isoform) expression between two groups of 10 animals with one lane per
> animal. I am using the public server to practice with some small data sets
> right now, but will be getting the real data very soon and plan on u
Sent: Tue 1/18/2011 9:29 PM
To: Martin, David A.
Cc: eaf...@emory.edu; galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] Galaxy for gene expression comparison
> I am comparing RNA expression in two groups of rats, a drug treated group
> against a control group. There are 10 biological re
> I am comparing RNA expression in two groups of rats, a drug treated group
> against a control group. There are 10 biological replicates in each group. I
> am unsure of how to flow this analysis through Galaxy using Tophat followed
> by Cufflinks/compare/diff. Should the files for each group
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