v2.5.1

New VASTDB library release to improve PSI quantifications.

NEW

• A new release of VASTDB libraries for all species (vastdb.sp.23.06.20).

  • These new libraries only involve changes in two files (Sp_COMBI-M-50-gDNA.eff and Sp_COMBI-M-50-gDNA-SS.eff), which are used by combine to quantify PSIs for alternative exons through the "a posteriori" and "annotated" modules, as well as for ALTA and ALTD events.
  • In these new files, a subset of pre-built exon-exon junctions was identified as likely to result in spurious mappings and thus excluded from the PSI quantifications by setting their mappability to 0. Spurious exon-exon junctions were identified using large sets of RNA-seq data for each species based on their mapped read distribution along the junction (in such spurious junctions, mapped reads accumulate only in the first or last positions of the exon-exon junction).
  • These new libraries are thus expected to reduce "skipping noisy" in PSI estimates, particularly for Hs2 and Mm2 (with nearly no effect for Hsa and Mmu).
  • There is no need to rerun align to generate updated PSI estimates. Re-running only combine on an existing align output is enough.
  • Different vast-tools versions and VASTDB libraries are retro- and forward- compatible.
  • To report version information in your Methods section, simply state the vast-tools and VASTDB library version you have used for combine (e.g. "we have used vast-tools v2.5.1 with the VASTDB library vastdb.hs2.23.06.20"). This information is stored in the VTS_LOG_commands.txt file.

• combine has a new option (--add_version) to add the vast-tools version to the output INCLUSION file name (e.g. INCLUSION_LEVELS_FULL-hg38-4-v251.tab). This option is off by default.

Updates and fixes

• These new libraries also include updated exon VastIDs for Hs2 and Mm2 (~500 and ~300, respectively) to more accurately match the lifted ones from Hsa and Mmu.

• Default value for --extra_eej option in combine has been set from 10 to 5.