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Question: create sqlite from cuffdiff terminal
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gravatar for dimitrischat
16 months ago by
dimitrischat • 0
dimitrischat • 0 wrote:

if there is a way to put an option when you run cuffdiff from terminal so that you can get an sqlite output? or to get the results from cuffdiff ( again by terminal ) and make an sqlite output. is there a way?
rna-seq • 411 views
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modified 16 months ago by Jennifer Hillman Jackson ♦ 25k • written 16 months ago by dimitrischat • 0
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gravatar for Jennifer Hillman Jackson
16 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

While Galaxy tools can be run line-command, we do not recommend running this particular tool with this option outside of Galaxy. Doing so will likely not produce the desired results.

Instead, run the tool within Galaxy. You can always download the output and use it locally.

If you program, the API could be one way to accomplish the task without needing to go through the GUI. Bioblend is a very popular choice: https://galaxyproject.org/develop/api/

Thanks! Jen, Galaxy team
ADD COMMENT • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k
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