Question

How to use the -swapstrands option in rpkmforgenes.py

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9.8 years ago

R ▴ 10

Hi,

Does anybody know which option should be used for strand-specific data when we use rpkmforgenes.py? -swapstrands?

RNA-Seq • 1.5k views

ADD COMMENT • link updated 9.6 years ago by Istvan Albert 100k • written 9.8 years ago by R ▴ 10

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strand specific, prepared using TruSeq Stranded RNA Kits (dUTP second strand marking)? So, should I use -swapstrands?

ADD REPLY • link 9.8 years ago by R ▴ 10

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I believe so, yes. You can always double check by just looking at things in IGV or a similar browser.

ADD REPLY • link 9.8 years ago by Devon Ryan 104k

score 0 · Answer 1 · 2014-07-21

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9.8 years ago

Devon Ryan 104k

It'll depend on how the library was made. It's either -strand or -swapstrands.

ADD COMMENT • link 9.8 years ago by Devon Ryan 104k