Question

Salmon libtype - Does it matter?

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7.7 years ago

Matthias ▴ 30

Hi,

I was wondering what happens if you have the libtype wrong for Salmon? Or why it requires that you supply it? I wasn't sure if the first read of my paired-end reads was forward (ISF) or reverse (ISR), so I ran it both ways, and the mapping efficiencies were identical between the runs.

Thanks, Matt

Salmon alignment • 6.6k views

ADD COMMENT • link 7.7 years ago by Matthias ▴ 30

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It is possible that your data was prepared by an unstranded kit/method. You can verify this by using the infer_experiment.py script from RSeQC as described here.

ADD REPLY • link 7.7 years ago by GenoMax 141k

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Thanks for the quick answer Rob, I appreciate it.

ADD REPLY • link 7.7 years ago by Matthias ▴ 30

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You're very welcome :).

ADD REPLY • link 7.7 years ago by Rob 6.5k

score 4 · Accepted Answer · 2016-08-18

Hi Matthias,

You can find a description of the behavior you're seeing, and why it's generally expected here. Also, I'll note that if you update to the latest release of Salmon (currently v0.7.0), available here, you can use the A (automatic) library type to have Salmon automatically infer the most-likely library type for you.