How should STAR define multimappers
Currently --outFilterMultimapScoreRange 1
is used, which is the default behavior. That means if a read maps to two regions with scores differing by 1, the read will be considered a multimapper mapping to those two regions. Should this be set to 0? e.g. if one region gives a non-shared maximum score, the read is considered a unique mapper, even if it maps to many other regions with a score just 1 lower than the max.
If we keep default behavior we should erase the argument from the rule for decluttering.