> 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 1.3.0   27th of May, 2019
    • New cmpr_features: for visual inspection + statistical testing of dependencies between features. For a given table with features, the user can plot the distribution of one feature (as boxplot) for bins of all data points. These bins are defined by quantiles of the data for each of the other features at a time. Special mode: If input table describes exons/introns and contains dPSI or PSI columns, then exon-/intron-related features are extracted automatically and the distribution of the dPSI or PSI feature is plot over the extracted exon/intron features.
    • Change get_vast: now outputs three more columns: mean PSI for grpA and gprB, and Wilcoxon test for comparing PSIs of group A vs group B.
    • Change get_vast: got extended to more robustly recognize types of splicing events (COMPLEX =~ /IR/i , /Alt3/i, /Alt5/i, -> rest are exons). Does not influcence how users use this command.
    • Perl shebang: now is #!/usr/bin/env perl
    • Rscript shebang: now is #!/usr/bin/env Rscript
    • Change get_efeature/get_ifeature: extended to allow the user to specify the gene-id-field in the GTF to be used for extracting gene ids.
    • Change cmpr_exons/cmpr_introns: adapted according to potential gene-id-field definition in get_efeatures/get_ifeatures.
    • Bugfix prnt_tab: now prints correctly table header in mode -W.
    • Bugfix retr_rnaseq: if wget failed to download SRA archives, then the prefetch method will be tried as backup download approach.
    • Bugfix add_header: does not assume anymore that there is already a header in the first line of the table to which a header should be added .

  • 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.