StringTie - Multimapped reads

Question

[sneha108.ss]

Hello,

I am using StringTie to assemble and quantify RNA seq reads. Could someone please help me understand how StringTie deals with multi-mapped reads? The manual states that the -M option "specifies the maximum fraction of multiple-location-mapped reads that are allowed to be present at a given locus" and that the default value is 0.95. I did not completely understand what this means.

Also, it will be really helpful if someone could explain how StringTie performs multi-mapping correction.

I am using StringTie version 1.3.4.

Thanks

Answer 1

[Kristoffer Vitting-Seerup]

From the methods section of the StringTie paper:

if a fragment aligns in n places, than that fragment alignment will contribute 1/n to the edge capacity