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Question: Trying to find antisense transcripts. Can Cufflinks in Galaxy specify library type?
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gravatar for jaeil.han
3.0 years ago by
jaeil.han • 10
United States
jaeil.han • 10 wrote:

Hello,

I am trying to find antisense transcripts, and mapping stranded reads to reference genome using Tophat (library type specified to fr). I wonder if I have to specify the library type in Cufflinks as well because I can't find the library type option in Cufflinks of Galaxy. I am afraid if I have to use command line to run Cufflinks with that option.

 

thanks!
cufflinks • 760 views
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modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by jaeil.han • 10
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gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Library type can be specified on the Galaxy Cufflinks form. Change Set advanced Cufflinks options to Yes, then the option Library prep used for input reads will be available.

Hopefully this helps! Jen, Galaxy team
ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k
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