Question: CummerRbund sqlite input file doesnt correspond to Cuffdiff output
0
gravatar for Wanderer
15 days 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 • 44 views
ADD COMMENTlink modified 15 days ago • written 15 days ago by Wanderer10
3
gravatar for Jennifer Hillman Jackson
15 days ago by
United States
Jennifer Hillman Jackson23k 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 15 days ago by Jennifer Hillman Jackson23k

Thank you so much! love you!!

ADD REPLYlink written 15 days ago by Wanderer10
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