Dear Subread team
I have some questions about Subread with -B option.
Since the multi-mapping reads are defined as reads with >1 equally-best mapping locations, what happens if I use the
-B <n> option to limit the number of mapping sites reported for Subread (or -nBestLocations in RSubread)? Are <n> mappings reported randomly?
How would you advice to use the -B option if my data as about 40-50% repeat mappings, and i wish to count all equally-best mapping locations for a read, in order to quantify repeats properly.
Also, how is this affected by -Q or -H options?