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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.
--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 : If specified, the RPM and RPKM will be normalized by the total number of reads mapped to all target regions. The default is to use all mapped reads (including off-target reads) for normalization
--exon_cout : read count for each exon. A read may be counted to multiple exons if this read is mapped to multiple exons.
--exon_cout : read count for each exon. A read may be counted to multiple exons if this read is mapped to multiple exons.
--gene_cout : read count for each gene.
--gene_cout : read count for each gene.
== Output files ==
== Output files ==
