> 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. _______________________________________________ galaxy-user mailing list [email protected] http://lists.bx.psu.edu/listinfo/galaxy-user
