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
Hi [Matthias](https://www.biostars.org/u/30561/),

  You can find a description of the behavior you're seeing, and why it's generally expected [here](https://github.com/COMBINE-lab/salmon/issues/67).  Also, I'll note that if you update to the latest release of Salmon (currently v0.7.0), available [here](https://github.com/COMBINE-lab/salmon/releases/tag/v0.7.0), you can use the `A` (automatic) library type to have Salmon automatically infer the most-likely library type for you.