Question: cuffdiff & cummerbund
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Keith E. Giles • 170 wrote:
I'm very surprised to see that the only available output for cuffdiff is now in the cummerbund compatible rsqlite db. I can't see any way to actually analyze that data in galaxy. Although I'm competent with bash, not as much w/ R. It seems to me now that there is no way to actually analyze your RNA-seq using cuffdiff in Galaxy. The only way is to download the Rsqllite db output and analzye it there. Isn't this contrary to the entire purpose of galaxy? Its a bit frustrating that the older version of Cuffdiff, which output tab-delimited text files was much easier to interface with other datasets either on the command line or in galaxy. Am I missing something here?
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modified 3.5 years ago
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Bjoern Gruening ♦ 5.1k
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3.5 years ago by
Keith E. Giles • 170
Oddly enough, a tool called 'CuffDiff for CummeRbund" produces all of the tabular outputs you're looking for and does not produce the sqlite file by default. Go figure
Even more oddly enough, a couple of tools, called "Extract_CuffDiff" and "Plot_CuffDiff" are advertised in the Galaxy Videos (see "NGS101-16 RNA-Seq: Playing with CuffDiff output and Cummerbund to find differentially expressed transcripts" here https://vimeo.com/128265982) but are implemented in the test.galaxyproject.org instance only and NOT in the usegalaxy.org instance. Release of "Extract_CuffDiff" function on Galaxy Main would solve the problem!
EDIT: I just noticed that the CuffDiff tool on GalaxyMain has been reverted to previous behaviour: it does not produce the sqldb anymore but the old 10-11 files (expression testing and FPKM trackings...). This is good news enough at least until the new "extract_CuffDiff" function will not be made available.