understanding inclevel

[Adi Gershon]

Hi i look at the equision of the inclevel colunm
ψ = (I/LI) / (I/LI + S/LS)
i perfectly understand it regrding to SE.
but i wanted to make sure i understand it correctly for other events
can you confirm this:
RI (Retained Intron)
Inclusion (I): Reads mapped to the intron, indicating retention.
Skipping (S): Reads spanning the exon-exon junction, indicating splicing of the intron.
IncLevel1 (ψ): Shows how often the intron is retained in sample 1.
IncLevel2 (ψ): Shows how often the intron is retained in sample 2.

and 
A5SS (Alternative 5' Splice Site)
Inclusion (I): Reads mapped to the longer splice isoform using the upstream 5' splice site.
Skipping (S): Reads mapped to the shorter splice isoform using the downstream 5' splice site.
IncLevel1 (ψ): Indicates how often the longer isoform is used in sample 1 compared to the shorter isoform.
IncLevel2 (ψ): Indicates the same for sample 2.

Im assuming the 3 is the same as the 5.

thank you

[kutsc...@gmail.com]

The diagram in the README shows which reads count toward the inclusion or skipping isoform of each event type: https://github.com/Xinglab/rmats-turbo/tree/v4.3.0?tab=readme-ov-file#output

The README also describes the different ways for a read to count toward one of the isoforms in the "Event specific columns" section which names the optional columns available when run with --individual-counts

What you wrote for RI events is correct. For A5SS, the diagram shows that the skipping counts come from reads with the splice junction of the shorter exon (short_to_flanking_count). The inclusion counts do not necessarily have the splice junction of the longer exon. An inclusion read could cover the short exon boundary without reaching the other splice junction (across_short_boundary_count) or the read could be contained within the portion of the exon after the short boundary (exclusive_to_long_count)

See also: https://github.com/Xinglab/rmats2sashimiplot/issues/68#issuecomment-910567403

Eric