Here is a changelog for the 2.0.0 version:
alignbecomes strand-aware. Before mapping, reads are automatically tested to infer whether they are strand-specific or not, and in which direction (FR or RF). Mapping is then performed according to this information. It is possible to run any fastq file in the non-strand-aware mode (
--ns), which is equivalent to running
combineincludes a new module that generates PSIs for all annotated exons (provided they fulfill some mappability and read balance requirements; see README for more information). These means the final INCLUSION table now contains tens of thousands of new exons, often with PSI ~ 100 (i.e. constitutive exons). They can be distinguish by the first digit of the event ID (e.g. HsaEX6000001).
IMPORTANT NOTE: these changes require new VASTDB files to be installed. In particular, strand-specific mapping requires different mappability files and the annotation module uses a new template. It is recommended that the entire libraries from version v1 are deleted, and the new libraries simply re-install them from scratch. You may download the new libraries for each available species here (you will only need to untar them afterwards and make sure they are inside VASTDB/):
- Human (Hsa): http://vastdb.crg.eu/libs/vastdb.hsa.16.02.18.tar.gz
- Mouse (Mmu): http://vastdb.crg.eu/libs/vastdb.mmu.16.02.18.tar.gz
- Chicken (Gga): http://vastdb.crg.eu/libs/vastdb.gga.16.02.18.tar.gz
- Zebrafish (Dre): http://vastdb.crg.eu/libs/vastdb.dre.16.02.18.tar.gz
- Sea urchin (Spu): http://vastdb.crg.eu/libs/vastdb.spu.16.02.18.tar.gz
- Planarian (Sme): http://vastdb.crg.eu/libs/vastdb.sme.16.02.18.tar.gz
Updates and fixes
- Quantification of multi-microexon events has been modified so that only reads fully covering a microexon are used to support inclusion. For Spu and Dre, exon-microexon or microexon-exon junction were removed also for simple microexon events. (This update was done to avoid false positive microexon calls that overlap with longer exons).
- It is possible to obtain the number of counts per exon-exon junction also for the microexon and transcript-based (exskX and MULTI3X) pipelines using the option
- The non-strand-specific mappability file for the MULTI pipeline in Mmu was updated.