Published on 30 August 2018, 17:59 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 2.1.0 version:
New features
- The ANNOT (annotated exons; ANN) module from `combine` uses a slightly different strategy to define complex skipping reads, which may result in different PSIs for some events. It is estimated to significantly (abs(deltaPSI) > 15) impact ~0.5% of the ANN events. This change has been implemented since it performed better with reads simulating transcripts with random skipping of constitutive exons. Therefore, it may improve quantifications particularly for 'artificial' conditions such as KDs of RNA biding proteins. While it has been shown to decrease the false negative rate in simulated data, it might slightly increase the false positive rate in real biological samples.
- A new module `compare_expr` has been included to identify differentially expressed genes based on fold changes of cRPKMs between samples. It uses a similar logic to the one used by `compare` to identify differentially alternatively spliced events.
- `compare` can provide all events (`--print_all_ev`) and all AS events (10<PSI<90 in at least one compared sample; `--print_AS_ev`) that pass the coverage criteria. It can also print different sets of events to facilitate their downstream comparison using Matt (http://matt.crg.eu/) (`--print_sets`):
- CS: all events with coverage and constitutively spliced (PSI>95 for AltEx, PSI<5 for IR).
- CR: all events with coverage and cryptically spliced (PSI<5 for AltEx, PSI>95 for IR).
- AS_NC: all events with coverage, alternative (10 < av_PSI < 90 in a group) and that do not change between the two conditions (abs(dPSI)< max_dPSI).
Updates and fixes
- trim5 option added on `align` to skip the first X nucleotides of the forward read. This is handy when there are ambiguous nucleotides that will result in no mapping in the strand determination step as well as in the gene expression quantification.
- Minor corrections and bug fixes.
- Updates in help messages and README.