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Salmon libtype - Does it matter?

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
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written by Matthias • Matthias

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.

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written by GenoMax GenoMax

Thanks for the quick answer Rob, I appreciate it.

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written by Matthias • Matthias

You're very welcome :).

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written by Rob Rob

1 answer

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.

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written by Rob Rob

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