A discussion of rmats2sashimiplot

[Yongqiang Xing]

Dear rMATs team:

       I run the "Test data" using the newest rmats2sashimiplot. I got the all results,but there some confusing problem. I give an example of GRHL1 as follows:

I run the Example of using sam files, drawing sashimiplot by rMATS format event files.  The command is "$rmats2sashimiplot --s1 ./testData/S1.R1.test.sam,./testData/S1.R2.test.sam,./testData/S1.R3.test.sam --s2 ./testData/S2.R1.test.sam,./testData/S2.R2.test.sam,./testData/S2.R3.test.sam -t SE -e ./testData/MATS_output/test_PC3E_GS689.SE.MATS.events.txt --l1 PC3E --l2 GS689 --exon_s 1 --intron_s 5 -o test_events_output", that is copied from the https://github.com/Xinglab/rmats2sashimiplot/

      The Sashimi_plot of GRHL1 can be downloaded from attachment. I found the IncLevel of every replicate is equal the  IncLevel of .\testData\MATS_output\test_PC3E_GS689.SE.MATS.events.txt. But the reads count in plot figure is different the reads count in .\testData\MATS_output\test_PC3E_GS689.SE.MATS.events.txt. I list the detail as follows:

In figure:

     GRHL1 PC3E: read count IC_SAMPLE_1 = (258,307,256) ;      SC_SAMPLE_1 =(5,0,2) ;        IncLevel1=0.948,1.0,0.98 

     GRHL1 GS689:read count IC_SAMPLE_2 = (20,35,23) ;          SC_SAMPLE_1 =(6,12,12) ;      IncLevel2=0.69,0.63,0.52

In .\testData\MATS_output\test_PC3E_GS689.SE.MATS.events.txt

     GRHL1 PC3E-1: read count IC_SAMPLE_1 = (208,284,235) ;  SC_SAMPLE_1 =(7,0,3) ;         IncLevel1=0.948,1.0,0.98

     GRHL1 GS689:  read count IC_SAMPLE_2 = (18,31,21) ;        SC_SAMPLE_2 =(5,11,12) ;     IncLevel1=0.69,0.63,0.52

.\testData\MATS_output\test_PC3E_GS689.SE.MATS.events.txt was downloaded from your website resource(http://www.mimg.ucla.edu/faculty/xing/rmats2sashimiplot/testData.tar). For convenience, I upload this file.

     I want to know what is the reason of read count difference. Meanwhile the IncLevel is equal. In this situation, which result can be used for futher research.

     I look forward your reply.

Best.

 

Thanks

[Yongqiang Xing]

在 2017年11月2日星期四 UTC-5下午10:04:05，Yongqiang Xing写道：