[BioC] summarizeOverlaps: number of dropped reads
Gabriele Schweikert
gschweik at staffmail.ed.ac.uk
Wed Apr 23 15:43:00 CEST 2014
Hello,
I'm using summarizeOverlaps with mode=union and inter.feature=TRUE to
count reads that overlap annotated features. This is great and exactly
what I need. However, I would also like to know how many reads are
dropped in this setting because they map to multiple features (as
opposed to reads not mapping to any of the annotated features.) Is
there an easy way to get this number?
I was thinking of counting again, this time with inter.feature=FALSE
and subtracting the results, but this is not quite what I want because
multiple reads are then also counted multiple times.
Thanks for the assistance
best wishes
Gabriele
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