rMATS Psi calculation: Does the OncoSplicing website describe rMATS Psi calculation correctly?

[X L]

Hi All,

I came across the description of rMATS PSI calculation on the OncoSplicing webpage (link here).

I’m wondering if the description is accurate. From my understanding, rMATS calculates PSI in two ways: JC and JCEC. It seems that the cartoon (attached here) describes only the JC method.

Additionally, I’m trying to understand the calculation of reads of inclusion isoform: Reads in = 0.5 * (b1 + b2) = 3. Is the 0.5 coefficient used here for length normalization?

Thanks,
Xiao

[kutsc...@gmail.com]

The description from that link seems to just be explaining how they calculated PSI and not explaining how rMATS calculates PSI. From that link:
> we modified the PSI calculation in the SplAdder project by normalizing the read quantification by the number of splice junctions

I think that "Reads in = 0.5*(b1 + b2) = 3" is using 0.5 to mean "divide by the number of junctions" and there are 2 junctions in the inclusion isoform

Eric

[X L]

Hi, Eric,

I see. Thank you for the clarification.

Best,

Xiao

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