The filtering algorithms can be applied to all the datasets or to user defined subsets. The default setting activates the filtering algorithms for the candidate intrachromosomal and extrachromosomal Bridge reads (SAME_CHR_DIFF_GENES and DIFF_CHR_DIFF_GENES datasets, respectively) and for the Anchor reads (HALF_MAPPED dataset). Note that Alternative Alignment, Hits threshold, Homology and A priori filters cannot be used to filter the Anchor reads dataset due to the peculiar characteristics of this dataset.