There are two scenarios:

1. When using the --intron exclude parameter, a read is counted ifit aligns to the exonic region of a gene (over 50% of the read length ismapped to the exonic region). Reads mapped to intronic or intergenicregions are not counted.

2. When using the --intron included parameter (the default), a read is counted if it aligns to the exonic or intronic regions of a gene (over 50% of the read length is mapped to these regions). Reads mapped to intergenic regions are not counted.