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Multivariate Analysis of Transcript Splicing (MATS)

Multivariate Analysis of Transcript Splicing (MATS)

Xing Lab, University of California, Los Angeles


  • 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.


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


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

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

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.

Software Download

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