Question: CummerRbund sqlite input file doesnt correspond to Cuffdiff output
0
gravatar for Wanderer
8 months ago by
Wanderer10
Wanderer10 wrote:

Is Cummerbund working right now? I tried to use but it is asking me the sqlite file, but cuffdiff doesnt output none sqlite file. How can I make it work?

Thank you!

galaxy cuffdiff • 275 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by Wanderer10
3
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

If you are running Cuffdiff outside of Galaxy, the Galaxy Cummerbund wrapper wouldn't be an appropriate choice. It expects output from the Galaxy Cuffdiff wrapper.

Two choices:

  • Run the Cuffdiff analysis in Galaxy and output the SQLite database. Do this by setting the option "Generate SQLite" to "yes" on the Cuffdiff tool form.

  • Use Cummerbund outside of Galaxy.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 8 months ago by Jennifer Hillman Jackson25k

Thank you so much! love you!!

ADD REPLYlink written 8 months ago by Wanderer10
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