python /media/shen/disk1/biosoft/rMATS.4.0.3beta/rMATS-turbo-Linux-UCS4/rmats.py --b1 mut.txt --b2 ctrl.txt --gtf /media/shen/disk1/jjc/reference/GRCm38/Mus_musculus.GRCm38.84.gtf --od mut/ -t paired --readLength 150 --nthread 40
head mut.txt
/media/shen/disk3/jjc/2019-8-9-R298P-endometriumRNA-seq-zy/combined/alignbam/S723-8_L1_J9038.bam,/media/shen/disk3/jjc/2019-8-9-R298P-endometriumRNA-seq-zy/combined/alignbam/S723-9_L2_J9085.bam,/media/shen/disk3/jjc/2019-8-9-R298P-endometriumRNA-seq-zy/combined/alignbam/S723-10_L2_J9049.bam
rmats2sashimiplot --b1 ../../../alignbam/S723-8_L1_J9038.bam,../../../alignbam/S723-9_L2_J9085.bam,../../../alignbam/S723-10_L2_J9049.bam --b2 ../../../alignbam/S723-1_L2_J9010.bam,../../../alignbam/S723-3_L2_J9043.bam,../../../alignbam/S723-4_L2_J9087.bam,../../../alignbam/S723-5_L2_J9031.bam,../../../alignbam/S723-6_L2_J9072.bam -t SE -e top20SE.MATS.JC.txt --l1 Mut --l2 control -o top20SE_plot
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