Question: How does Salmon handle reads that map to multiple locations that each have full coverage?
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gravatar for cameron.holman
16 months ago by
cameron.holman10 wrote:

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!

rna-seq mapping salmon dea • 382 views
ADD COMMENTlink written 16 months ago by cameron.holman10
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