Dear list,
I was wondering if is there is a way to apply the reduce function on a  GappedAlignments object according to the levels of a factor (such as the read ID from paired end data). I am basically trying to deal with the instance when the GappedAlignments object was obtained by reading a bam file obtained from a bowtie2 alignment on Illumina paired end data. Since both ends of the read get an entry in the bam file, I do not want to count twice the read when using later the function countOverlaps.
Thank you,
Adi Tarca

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