Difference Of 'Non-Primary Hits' And Multiple Mapped

Question

[Phil S.]

Hi there,

I am curious what is, using TopHat2, the difference between 'non-primary hits' and 'multiple mapped' after mapping?

Thanks in advance,

best

Phil

[Phil S.]

or are those just the same and I got confused?

Answer 1

[Devon Ryan]

If a read has non-primary alignments (and this aren't due to using the "fusion" option) then it's also a multi-mapper. Whether multimappers will also have non-primary alignments depends on the settings you use.

[Phil S.]

thanks for the fast answer!