Thanks for the information.
I've added an option to the Cuffdiff tool so that the read group files can be
output by Galaxy; this should make it possible to run Cuffdiff in Galaxy and
then Cummerbund for replicate analysis. This change will make it out to our
public server in a couple weeks.
T
In the past, others have had success using Cummerbund with Galaxy, and there's
even a Cummerbund wrapper in the tool shed:
http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund
That said, it appears that replicate information is largely contained in the
read group tracking files, which are no
I'm trying to run Cuffdiff on a set of 10 human samples with biological
replication then download the results for further analyses in
Cummerbund(v2.1.1). It seems like a standard workflow but I cannot get
cummerbund to acknowledge replicates. I download and rename the 11 cuffdiff
output files
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