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If the bam file is imported, you need to select the assembly with which the reads were aligned to, and which annotation model file you will use to quantify from the drop-down menus (Figure 2).

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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.

Min reads optioin is a filter, by default only the features whose sum of the reads across all  samples that are greater than  or equal to 10 will be reported. To report all the features in the annotation file,  set the value to 0.

If the Report unexplained regions check button is selected, an additional report will be generated on the reads that are considered not compatible with any transcripts in the annotation provided. Based on the Min reads for unexplained region cutoff, the adjacent regions that meet the criteria are combined and region start and stop information will be reported.

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