rMATS

Notes about the paper

New statistical model and computer program designed for detection of differential alternative splicing from replicate RNA-seq data.

sensitive to outliers

How to run rMATS code?

Download gitrepo: https://github.com/Xinglab/rmats-turbo/releases/tag/v4.1.1

Install it from the rmats folder and run:

./build_rmats

The test script that creates a conda environment doesn’t work but the main script works

Need fastq or bam files (paired or not), a gtf annotation file and a STAR binary indices containing the SA file (if using fastq)

python ../../rmats_turbo_v4_1_1/rmats.py --b1 bam1.txt --b2 bam2.txt --gtf ~/Annotation_file_gtf/gencode.v38.annotation.gtf -t paired --readLength 50 --nthread 8 --od output/ --tmp tmp/

An example of result:

EventType	TotalEventsJC	TotalEventsJCEC	SignificantEventsJC	SigEventsJCSample1HigherInclusion	SigEventsJCSample2HigherInclusion	SignificantEventsJCEC	SigEventsJCECSample1HigherInclusion	SigEventsJCECSample2HigherInclusion
SE	36	64	0	0	0	1	1	0
A5SS	19	23	0	0	0	0	0	0
A3SS	24	30	0	0	0	1	0	1
MXE	10	46	0	0	0	0	0	0
RI	76	102	5	4	1	4	1	3

SE = skipped exon
MXE = mutually exclusive exons
A3SS = alternative 3’ splice site
A5SS = alternative 5’ splice site
RI = retained intron

Rmatsashimiplot

Rmatsashimiplot is a git repo that permits to create sashimiplot of the result of rmats

Installation of rmats2sashimiplot

Download the git repo

If using python3, you need to convert python2 script to pyton3 by running:

./2to3.sh -W

Then install it

python ./setup.py install

Example

It need bam/sam files, the coordinates to focus or the row lines of a specific event.

RI.MATS.JC_selected.txt example focusing on VIM gene:

ID	GeneID	geneSymbol	chr	strand	riExonStart_0base	riExonEnd	upstreamES	upstreamEE	downstreamES	downstreamEE	ID	IJC_SAMPLE_1	SJC_SAMPLE_1	IJC_SAMPLE_2	SJC_SAMPLE_2	IncFormLen	SkipFormLen	PValue	FDR	IncLevel1	IncLevel2	IncLevelDifference
3497	ENSG00000026025.16	VIM	chr10	+	17235168	17236379	17235168	17235389	17235845	17236379	3497	1,3	3,4	0,0	2,0	98	49	1	1	0.143,0.273	0.0,NA	0.208
3498	ENSG00000026025.16	VIM	chr10	+	17235845	17236379	17235845	17235889	17236293	17236379	3498	4,3	1,2	0,0	1,1	98	49	5.36756132241E-06	0.000407934660503	0.667,0.429	0.0,0.0	0.548

Example of command:

rmats2sashimiplot --b1 231ESRP.25K.rep-1.bam,231ESRP.25K.rep-2.bam --b2 231EV.25K.rep-1.bam,231EV.25K.rep-2.bam -t RI --l1 TestA --l2 Test2 -o output2/ -e output/RI.MATS.JC_selected.txt

The output is: