I'm trying to work through how Salmon deals with multi-mappers. It's clear how Salmon deals with reads that map to one transcript with full coverage and another that has gaps; the read will be assigned to the transcript with full coverage. I'm still not clear on how Salmon will deal with multi-mapping reads that map to multiple locations with full coverage.
In the case that Transcript A has gaps in coverage and Transcript B has full coverage, a read that maps to both A and B will be assigned to B. However, if Transcript A has full coverage and Transcript B has full coverage, how does Salmon handle a read that maps to both A and B? Furthermore, how does Salmon handle it if the read maps to 3+ locations with full coverage?
Thanks for your help!
