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vast-tools v1.0.0-beta.2
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@kcha kcha released this 23 Nov 15:51
· 669 commits to master since this release
v1.0.0-beta.2
ae7cb3f

This update contains some bug fixes from v1.0.0-beta.1.

New

  • A new method to calculate intron retention is available (use --IR_version 2 in align and combine). It is a modification of the original one (as described in Braunschweig et al, 2014), but uses multi exon-exon junction read counts for skipping. It provides a more realistic estimate of the Percent Intron Retention (PIR) at the gene level. The original method can still be used with --IR_version 1.

    • New files are needed in the VASTDB/Species/FILES/ folder for the new IR option as well as to obtain gene IDs for GO analysis. Additional files for human, mouse and chicken can be downloaded here: http://vastdb.crg.eu/libs/PATCH_IRv2.tar.gz. To install the patch:
    tar -xzvf PATCH_IRv2.tar.gz
rsync -av PATCH_IRv2/ /path/to/VASTDB/

  • merge: a new module to merge align outputs from multiple subsamples into new sample files.

  • compare: a new module to identify differentially spliced (DS) AS events based on average inclusion level differences. It also provides gene lists for GO analysis and directly plots DS AS events. This module is independent of diff and is not a replacement for it.

Updates and fixes

  • Fix in the calculation of gene expression (cRPKMs) to properly account for read length. A new option --readLen or a specific sample name format (Sample-readLen.fq.gz) is enforced in align.
  • Definition of species (--sp) is enforced in combine.
  • Fix in combine. Some Alt3 and Alt5 AS events were not being outputted if their coordinate matched that of a cassette exon.
  • Fix in ylim setting in plot.
  • Update of install.R for the new VASTDB libraries.
  • Update of documentation.
  • Misc. updates.
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