Illustration of the three types of strand specific assays on paired end reads. _R1 and _R2 means read first-in pair and second-in-pair respectively. Arrows indicate strand directions.
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Minimum read overlap with feature can be specified in percentage of read length or number of bases. By default, a read has to be 100% within a feature. You can allow some overhanging bases outside the exonic region by modifying these parameters.