Multivariate Analysis of Transcript Splicing (MATS)
Updates
- 05/01/2017
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Release of rMATS-docker 0.1beta
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Beta release of a much faster and slimmer version of rMATS in docker container.
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All required packages are packed in the docker container.
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Counting procedure is 20-100 times faster.
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Statistical part is 300-500 times faster.
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Intermediate files are ~1000 times smaller.
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- 08/18/2016
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Release of rMATS 3.2.5
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Added support for multiple versions of samtools. rMATS was tested with samtools v1.2 and v1.3.1.
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- 07/29/2016
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Release of rMATS 3.2.4
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Improved and faster counting procedure.
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Improved numerical optimization.
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Improved prerequisites validation.
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Optional detection of novel splice sites (unannotated splice sites).
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- 05/02/2016
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Release of rMATS 3.2.2.beta
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Changed default aligner to STAR: rMATS now aligns fastq files with STAR.
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- 03/03/2016
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Release of rMATS 3.2.1.beta
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Fixed a bug related to read counting of short exons.
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- 02/12/2016
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Release of rMATS 3.2.0.beta, a major update with important features added to rMATS:
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Detection of novel splice sites and novel exons: rMATS now finds novel splice sites and novel exons.
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Detection of micro-exons: rMATS now detects micro-exons involved in AS events.
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Strand-specific data: rMATS now works with strand-specific data.
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Multi-exon (N>2) spanning reads: rMATS now handles junction reads that span more than 2 exons.
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rMATS now works with most recent version of samtools (tested with samtools v1.2).
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- 2/25/2015
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Release of rMATS 3.0.9,
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Increased the stability of numerical optimization.
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Deprecated -expressionChange option.
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- 11/26/2014
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Official announcement for the release of replicate MATS (rMATS):
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We have developed replicate MATS (rMATS) to detect differential alternative splicing from replicate RNA-seq data.
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MATS 3.0.0 and beyond is rMATS. Please download the latest version (currently MATS 3.0.8) from our website.
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- 04/09/2014
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Release of PrimerSeq,
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We released a primer design tool, PrimerSeq, for designing RT-PCR primers from MATS output.
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- 8/26/2013
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Release of MATS 3.0.8,
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Improved the optimization procedure for the paired replicate model.
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- 11/16/2012
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Release of MATS 3.0.6.beta,
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Fixed a bug related to handling TopHat 2.x.x or Bowtie 2.x.x output.
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Fixed a ‘wc’ command bug related to running MATS on MacOS, thanks to Peter Stoilov for pointing this out.
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- 11/7/2012
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Release of MATS 3.0.5.beta,
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BAM files from TopHat 2.x.x or Bowtie 2.x.x now work properly.
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- 10/18/2012
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Release of MATS 3.0.4.beta,
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Fixed a bug related to gene expression level calculation.
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- 10/12/2012
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Release of MATS 3.0.3.beta,
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Fixed a bug related to gene expression level calculation.
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- 8/30/2012
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Release of MATS 3.0.2.beta,
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Fixed a bug related to default insert sizes and standard distribution.
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- 8/24/2012
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Release of MATS 3.0.1.beta,
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A bug related to Ubuntu (tested on 12.04) is fixed.
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- 8/9/2012
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Release of MATS 3.0.0.beta, a major update with important features added to MATS:
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Replicate data support: MATS now works with replicate RNA-Seq data from both paired and unpaired study design.
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Improved filtering system: MATS now filters out AS events where large gene expression fold changes may confound the analysis.
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MacOS support: MATS now supports both Linux and MacOS (tested on MacOS 10.8.1).
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- 5/25/2012
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Release of MATS 2.1.0
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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.
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A bug related to an empty AS event file is fixed.
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- 5/15/2012
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Release of MATS 2.0.0, a major update with important features added to MATS:
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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.
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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.
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Improved statistical power: MATS now works with both exon-exon junction reads and exon body reads which leads to improved statistical power.
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- 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.
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- 2/16/2012
- Release of MATS 1.1.0, adds Ensembl version of mouse annotation.
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- 12/15/2011
- Release of MATS 1.0.0, the initial version of MATS was opened.
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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
Documentation
rMATS Companion
- rMATS-STAT: standalone statistical model to test for differential splicing.
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Questions/Comments