Differential RNA splicing analysis using rMAT

Summary

Differential splicing analysis using rMAT, one of the best tools.

Only works hg38.

Input

Example data dir: Projects/Siqi_data/RNAseq_data/Differential_Exon_Analysis/test

1. bam.tsv

3-col tsv, col1 is group1 bam files, seperated by commna. col2 is group2 bam files. col3 is comparison label.

GFP_pos_S2.markdup.uq.bam,GFP_pos_S3.markdup.uq.bam,GFP_pos_S8.markdup.uq.bam   GFP_neg_S18.markdup.uq.bam,GFP_neg_S19.markdup.uq.bam,GFP_neg_S20.markdup.uq.bam        GFP_pos_neg
H1_S1.markdup.uq.bam,H1_S3.markdup.uq.bam,H1_S5.markdup.uq.bam  H2_S2.markdup.uq.bam,H2_S4.markdup.uq.bam,H2_S6.markdup.uq.bam  H1_H2
SRR5890882_Fetal_d11.markdup.uq.bam,SRR5890883_Fetal_d11.markdup.uq.bam SRR5890878_Adult_d11.markdup.uq.bam,SRR5890879_Adult_d11.markdup.uq.bam FA11
SRR5890884_Fetal_d14.markdup.uq.bam,SRR5890885_Fetal_d14.markdup.uq.bam SRR5890880_Adult_d14.markdup.uq.bam,SRR5890881_Adult_d14.markdup.uq.bam FA14

Usage

make sure your readlength match --readLength 101.

    hpcf_interactive

module load python/2.7.13

run_lsf.py -f bam.tsv --readLength 101 -p rMAT

Output

Results are stored in the $jid folder. Both paired-test (folder $COL3.RMATS.paired) and unpaired-test (folder $COL3.RMATS.unpaired) results are generated. If your data is unpaired, ignore it. Main result is *.MATS.JC.txt

code @ github.