Please help me with the fate of multimapping reads in the RNA-seq context

Question

[seta]

Hi all,

I read a sentence in a book about RNA-seq analysis, it says "Some aligners are able to distribute multimapping reads proportionally to the coverage between the equally matching locations".

Distributing of maultimapping reads based on the coverage between the equally aligned locations got me confused. Could anybody please explain a bit to me?

Thanks

[h.mon]

This sounds like an expectation-maximization approach to multi-mapping reads. I am not aware of any aligner doing this, though EM algorithms are common when counting multi-mapped reads (e.g. RSEM).

What is common among aligners is to randomly choose one location among the many equally good possible locations, but this is simpler than an EM algorithm.

edit: I should have googled before posting, here is a pre-print about EM-mapping.