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Multivariate Analysis of Transcript Splicing (MATS)

Multivariate Analysis of Transcript Splicing (MATS)

Xing Lab, University of California, Los Angeles

Updates

  • 11/26/2014
    • Official announcement for the release of replicate MATS (rMATS):
      • We have developed replicate MATS (rMATS) to detect differential alternative splicing from replicate RNA-seq data.
      • MATS 3.0.0 and beyond is rMATS. Please download the latest version (currently MATS 3.0.8) from our website.
  • 04/09/2014
    • Release of PrimerSeq,
      • We released a primer design tool, PrimerSeq, for designing RT-PCR primers from MATS output.
  • 8/26/2013
    • Release of MATS 3.0.8,
      • Improved the optimization procedure for the paired replicate model.
  • 4/5/2013
  • 11/16/2012
    • Release of MATS 3.0.6.beta,
      • Fixed a bug related to handling TopHat 2.x.x or Bowtie 2.x.x output.
      • Fixed a ‘wc’ command bug related to running MATS on MacOS, thanks to Peter Stoilov for pointing this out.
  • 11/7/2012
    • Release of MATS 3.0.5.beta,
      • BAM files from TopHat 2.x.x or Bowtie 2.x.x now work properly.
  • 10/18/2012
    • Release of MATS 3.0.4.beta,
      • Fixed a bug related to gene expression level calculation.
  • 10/12/2012
    • Release of MATS 3.0.3.beta,
      • Fixed a bug related to gene expression level calculation.
  • 8/30/2012
    • Release of MATS 3.0.2.beta,
      • Fixed a bug related to default insert sizes and standard distribution.
  • 8/24/2012
    • Release of MATS 3.0.1.beta,
      • A bug related to Ubuntu (tested on 12.04) is fixed.
  • 8/9/2012
    • Release of MATS 3.0.0.beta, a major update with important features added to MATS:
      • Replicate data support: MATS now works with replicate RNA-Seq data from both paired and unpaired study design.
      • Improved filtering system: MATS now filters out AS events where large gene expression fold changes may confound the analysis.
      • MacOS support: MATS now supports both Linux and MacOS (tested on MacOS 10.8.1).
  • 5/25/2012
    • Release of MATS 2.1.0
      • MATS now works with both read sequence files (fastq) and mapped reads files (bam). Using bam files adds flexibility in mapping because MATS will skip the read mapping step.
      • A bug related to an empty AS event file is fixed.
  • 5/15/2012
    • Release of MATS 2.0.0, a major update with important features added to MATS:
      • Simplified running procedure: MATS now only requires the raw RNA-Seq data, a genome sequence file, and a gene/transcript annotation file in GTF format as the input.
      • Ability to analyze different types of alternative splicing events: MATS now automatically detects and analyzes alternative splicing events corresponding to all major types of alternative splicing patterns.
      • Improved statistical power: MATS now works with both exon-exon junction reads and exon body reads which leads to improved statistical power.
  • 3/5/2012
    • Release of MATS 1.2.0, added a new method to calculate P-values by likelihood-ratio test, which is ~100x faster than the Bayesian method.
  • 2/16/2012
    • Release of MATS 1.1.0, adds Ensembl version of mouse annotation.
  • 12/15/2011
    • Release of MATS 1.0.0, the initial version of MATS was opened.



Documentation

Citation

Shen S., Park JW., Lu ZX., Lin L., Henry MD., Wu YN., Zhou Q., Xing Y. rMATS: Robust and Flexible Detection of Differential Alternative Splicing from Replicate RNA-Seq Data. PNAS, 111(51):E5593-601. doi: 10.1073/pnas.1419161111

Park JW., Tokheim C., Shen S., Xing Y. Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS. Methods in Molecular Biology: Deep Sequencing Data Analysis, 2013;1038:171-179 doi: 10.1007/978-1-62703-514-9_10

Shen S., Park JW., Huang J., Dittmar KA., Lu ZX., Zhou Q., Carstens RP., Xing Y. MATS: A Bayesian Framework for Flexible Detection of Differential Alternative Splicing from RNA-Seq Data. Nucleic Acids Research, 2012;40(8):e61 doi: 10.1093/nar/gkr1291

About MATS

MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design.



Software Download
  • Bowtie indexes download for Human (hg19) and Mouse (mm9)

Pre-requisites

Contact

Correspondences regarding the rMATS algorithm should be directed to Prof. Yi Xing (yxing at ucla.edu) and Shihao Shen (shihao at ucla.edu).

Correspondences regarding running of the rMATS pipeline should be directed to Juw Won Park (jwpark2012 at ucla.edu).