The N filter is activated by default. The filtering applies to the sequence of each SAM or BAM read. If the number of undetermined nucleotides within a read is equal or lower than the N threshold filter (red arrow), the pair is discarded.

The Hits filter is activated by default. This filter is run on candidate Bridge reads only after the identification of the genes associated to each pair. If the number of events bridging to two genes is lower than the Hits threshold (red arrow), each pair bridging to those genes is discarded.