Interpretation of MXE results

[Mutnuru Srinivas Abhishek 1920110]

Hi,

I had recently used rMATS for analysing my RNA-seq data and I was trying to understand how to interpret the MXE results. 

Please let me know if the following consideration of mine is correct.

If the its Chr "+" then the IJC_Sample1 which is inclusion, is of the exon stated as 1st exon and if its Chr  "-" then IJC_Sample1 is of exon stated as 2nd Exon. Is this correct?

Please help me out

Thank you

Sincerely,

Abhishek 

[kutsc...@gmail.com]

Yes, MXE "+" strand inclusion is for the 1st exon, and MXE "-" strand inclusion is for the 2nd exon

https://github.com/Xinglab/rmats-turbo/tree/v4.3.0?tab=readme-ov-file#output
> IJC_SAMPLE_1: Inclusion counts for sample 1. Replicates are comma separated
> If the strand is +, then the inclusion form includes the 1st exon (1stExonStart_0base, 1stExonEnd) and skips the 2nd exon
> If the strand is -, then the inclusion form includes the 2nd exon (2ndExonStart_0base, 2ndExonEnd) and skips the 1st exon

Eric

[kutsc...@gmail.com]

See this post about interpreting IncLevelDifference: https://github.com/Xinglab/rmats-turbo/issues/508