Changes

  --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

  --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.

  --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.