> 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 now, I would suggest doing this for making 
> calls with no novel genes:
> 
> 1) upload your reads
> 2) fastq groom them into sanger format
> 3) run tophat on each lane individually
> 4) run cuffcompare with the gtf file you downloaded from uscs or wherever 
> against itself, 
> this puts it in a nice format to use with cuffdiff
> 5) merge the bam files from tophat for the 10 lanes from each group into one 
> file
> 6) run cuffdiff using the transcript gtf output file from cuffcompare and the 
> two merged bam files

You can also run this workflow easily enough for de novo transcripts as well; 
only change is whether Cufflinks is fed a reference GTF.

> 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.

Yes, looking into this soon.

J.
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