Question: cuffdiff & cummerbund
gravatar for Keith E. Giles
3.5 years ago by
United States
Keith E. Giles170 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?

galaxy • 1.8k views
ADD COMMENTlink modified 3.5 years ago by Bjoern Gruening5.1k • written 3.5 years ago by Keith E. Giles170

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

ADD REPLYlink written 3.5 years ago by madkisson30

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 but are implemented in the instance only and NOT in the 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.

ADD REPLYlink modified 3.5 years ago • written 3.5 years ago by rossi0
gravatar for Bjoern Gruening
3.5 years ago by
Bjoern Gruening5.1k
Bjoern Gruening5.1k wrote:

Hi Keith,

you need to have this tool available:

It will extract you all needed information as before. See also this discussion here:

If you have cummerbund around ( you can also produce a lot of pictures from your sqlite storage.



ADD COMMENTlink written 3.5 years ago by Bjoern Gruening5.1k
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