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.