Hello Irene, On 7/16/12 4:11 PM, Irene Bassano wrote:

Hi, just few questions about cuffdiff if anyone can answer:

1.how can I load more than two sam/bam files?Galaxy gives spaceonly for two files

Change the tool form for the option "Perform replicate analysis:" to be "Yes" (the default is "No"). Use two conditions (Groups).

2.what to use as input: cufflinks, cuffcompare or cuffmerge?

GTF output from any of these may be appropriate. Please see the tutorial on Galaxy main at: http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise FAQ: http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq And the "Common uses" protocols on the Cufflinks web site plus their new paper (also linked at this site, from side bar, as "Protocol"): http://cufflinks.cbcb.umd.edu/tutorial.html Best, Jen Galaxy team

Thanks a lot!

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