MATS 4.0.2

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.

Accessing the software

To load the module:

$ module load MATS/4.0.2-foss-2018a

An example command to include in your job script:

python $MATS_ROOT/RNASeq-MATS.py \
    -s1 $MATS_ROOT/testData/231ESRP.25K.rep-1.R1.fastq:\
$MATS_ROOT/testData/231ESRP.25K.rep-1.R2.fastq,\
$MATS_ROOT/testData/231ESRP.25K.rep-2.R1.fastq:\
$MATS_ROOT/testData/231ESRP.25K.rep-2.R2.fastq \
    -s2 $MATS_ROOT/testData/231EV.25K.rep-1.R1.fastq:\
$MATS_ROOT/testData/231EV.25K.rep-1.R2.fastq,\
$MATS_ROOT/testData/231EV.25K.rep-2.R1.fastq:\
$MATS_ROOT/testData/231EV.25K.rep-2.R2.fastq \
   -gtf $MATS_ROOT/testData/test.gtf -bi $STAR_INDEX/hg19 -o out_test -t paired \
   -len 50 -a 1 -c 0.0001 -analysis U -keepTemp

This runs the Python script RNASeq-MATS.py on the test data supplied with MATS using the hg19 STAR index that is installed with MATS.

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

Previous versions of this application are recorded below:

Known Problems & Limitations

None.

Other Information

The Support Level for this application is An.

Visit the MATS website for more information regarding this application


Last modified: 31 October 2018