Published on 17 October 2018, 12:00 by Webadmin —
A new version of vast-tools has been released. You can find it in our GitHub repository.
Here is a changelog for the 2.1.3 version:
New features
- `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.