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--min_overlap : minimum number of bases overlapping an input region to consider that the read is in the region.
--min_overlap : minimum number of bases overlapping an input region to consider that the read is in the region.
--min_map_quality : reads with map quality below this number will be ignored
--uniq : If a read is mapped to multiple regions (e.g. exons) this read will be counted only once toward the read count in the gene
--uniq : If a read is mapped to multiple regions (e.g. exons) this read will be counted only once toward the read count in the gene
--norm_by_mapped2target : The RPM and RPKM will be normalized by reads mapped only to target regions. Default is to use all mapped reads in a bam file.
--norm_by_mapped2target : The RPM and RPKM will be normalized by reads mapped only to target regions. Default is to use all mapped reads in a bam file.
