v2.1.3

NEW

• compare has a new option, --use_int_reads, to increase the stringency when calling differentially regulated intron retention events. It requires that the average number of corrected intron body read counts of the group with the higher PIR is at least 0.4 times the average of the exon-intron junction reads (used to calculate PIR). This fraction can be modified using --fr_int_reads. Intron body reads come from mapping reads to 200bp in the middle of the intron, or the whole intron when shorter. (This mapping was already implemented from the first release of vast-tools, but only used when doing the binomial test for the balance score [5th score in IR]. Therefore, there is no need to re-run align to have access to this feature, only combine; see next).

• combine has a few changes to include the corrected number of reads in the quality score for IR (3rd score). Also, the 4th score now has the corrected number of read for EI, IE and EE, not the raw counts.