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rMATS-ISO

What is rMATS-ISO ?

rMATS-Iso is a generalization of the rMATS statistical framework, and the first event-based tool which can detect differential AS in splicing modules with complex splicing patterns using replicate RNA-seq data. The rMATS-Iso statistical model utilizes a hierarchical framework to account for both the estimation uncertainty in PSI values in individual replicates as well as the variation among replicates.

rMATS-ISO

Table of Contents

Installation

Operating system

rMATS-ISO currently can only be built and run on Linux/Unix systems.

Cloning and building rMATS-ISO pipeline

git clone https://github.com/Xinglab/rMATS-ISO.git --recursive
cd rMATS-ISO
make
export PATH=$PATH:$PWD/lr2rmats/bin # To permanently modify your PATH, you need to add it to your ~/.profile or ~/.bashrc file.

Python 3 is required for installnation. After the building is done, the path of rMATS-ISO/lr2rmats/bin needs to be added to the environment variable PATH.

Components

rMATS-ISO consists the following components: lr2rmats, IsoModule, rMATS-EM, IsoClassify, and IsoPlot.

They will all be automatically downloaded and built via make command.

Getting started with test example in test_data

python ./rMATS-ISO.py --in-gtf ./test_data/gtf/PC3E_GS689.gtf --in-bam ./test_data/PC3E_GS689_short_read_bam_input.list -o ./output2/

All the output files and intermediate files will be generated in ./output folder.

Output folder

The test output folder will contain these following sub-folders:

ISO_module/
EM_out/

The Iso_module folder contains the detected splicing modules in files ended with IsoExon. The first line of each module contains the module ID, number of exons in the module, the number of isoforms, strand, chromosome, and gene name. The second line contains the exon coordinates. The rest lines contains the isoform definations in each row, including the how the exons are included in the module and how exons are connected in the isoform. Each row is an isoform.

ASM#0   4   3   +   chr2    MYO1B   ENSG00000128641 A
192265108,192265194 192265475,192265561 192267358,192267444 192272841,192272915 
4   0   1   2   3
3   0   2   3
2   0   3

The sample-specific read counts for each module are in files ended with IsoMatrix. The first line of each module contains the module ID, the number of patterns that a read can be overlapped with multiple isoforms, the number of isoforms, the left and right side length added to the module for reads to be fully covered.

Note that for a total of N isoforms, the maximum number of overlap patterns is 2^N-1, for reads to be overlapped with different combinations of isoforms.

ASM#0   5   3   219 135
101 776 0   0   1
101 157 0   1   0
101 133 1   0   0
101 101 1   1   0
101 1802    1   1   1

The EM_out folder contains the p values for the differential splicing of modules between two sample groups and a few additional parameters from the samples.

The p value for the differnetial splicing of splicing module is in the 6th column.

ASM_name total_isoforms total_exons total_read_count_group_1 total_read_count_group_2 p_value test_statistic isoform_inclusion_group_1 isoform_inclusion_group_2 isoform_inclusion_constrained variance_group_1 variance_group_2 variance_constrained dirichlet_parameter_group_1 dirichlet_parameter_group_2 dirichlet_parameter_constrained paired_isoform_pvalues isoform_index merge_info 
ASM#0 3 4 8904 6839 3.02868841117743e-13 61.347670914598 0.0686352968371457 0.575591066075565 0.277663108213901 0.000524292503279509 0.00139804133727612 0.0382402301701812 8.29974021020214 100 1.17865302356842 0.00138 1 NA

Contact

Shihao Shen shens@email.chop.edu
Yi Xing xingyi@email.chop.edu

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