> Matt Versions and Changes

A Unix toolkit for analyzing genomic sequences
with focus on down-stream analysis of alternative splicing events

       All & change log
  • Matt 1.2.1   28th of September, 2018
    • Change cmpr_exons/cmpr_introns: PDF reports contain now the reference to the Matt paper.
    • Bugfix in extr_scafids: now works correctly in mode GTF (before it was an endless loop)

  • Matt 1.2.0   1st of June, 2018
    • Change rna_maps/rna_maps_cisbp: Now, when users have defined a significance threshold, two PDF reports will be created. One with all motif RNA-maps, and a second one only with RNA maps with significant enrichment of motifs.
    • Change get_vast: simplified usability. Now, outputs all events from a VAST-TOOLs table with augmented information on PSI, dPSIs, PSI margins between PSI group a vs b, PSI range, etc. For the sub-selection of events, users might use get_rows are immediately apply def_cats. The standard workflow looks like: 1.) get_vast ... 2.) def_cats ... 3.) any high-level analysis.
    • Change get_vast: By default does not extract gene ids anymore. To do so, users can provide any gene annotation as GTF with parameter -gtf and gene ids will be retrieved automatically.
    • Change cmpr_exons/cmpr_introns: PDF reports contain now an overview section with significant results. Soignificance threshold can be controlled with argument -p PVAL.
    • Change get_efeatures/get_ifeatures: If FASTA file is unavailable, users can set its path to NA and will get all features but sequence related features.
    • New retr_geneids: Retrieve gene ids from any GTF for exons, introns, genes with known genomic locations.
    • Bugfix in rna_maps and rna_maps_cisbp: Corrects enrichment score in regions with low data coverage. Regions with 100% data coverage were unaffected.

  • Matt 1.1.0
    • First public version.

  • Matt 1.0.0
    • First version for CRG internal use only.