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How to find the Percent Spliced In (PSI) values in the rMATS? #444

Open Motoufiq opened 1 week ago

Motoufiq commented 1 week ago

Hello,

I am currently using the nf-core rnasplice module (https://nf-co.re/rnasplice/1.0.4), which includes rMATS. Could you please advise where I can locate the Percent Spliced In (PSI) values after running the pipeline? I’ve checked the rMATS output folder but haven’t found them.

rMATS typically generated several output files, such as:

.MATS.JC.txt (Junction Counts only) .MATS.JCEC.txt (Junction Counts and Exon Counts)

This is an example of the headers in my output: ID | GeneID | geneSymbol | chr | strand | exonStart_0base | exonEnd | upstreamES | upstreamEE| downstreamES | downstreamEE | ID | IJC_SAMPLE_1 | SJC_SAMPLE_1 | IJC_SAMPLE_2 | SJC_SAMPLE_2 | IncFormLen | SkipFormLen | PValue | FDR | IncLevel1 | IncLevel2 | IncLevelDifference |

Does IncLevel1 and IncLevel2 are PSI values for condition 1 (e.g., treatment group) and PSI values for condition 2 (e.g., control group)? IncLevelDifference is the difference between them?

EricKutschera commented 1 week ago

The IncLevel columns are PSI values. IncLevel1 has the PSI values for the inputs given in --b1 (or --s1) and IncLevel2 has the PSI values for the inputs given in --b2 (or --s2)

From https://github.com/Xinglab/rmats-turbo/tree/v4.3.0?tab=readme-ov-file#output IncLevelDifference: average(IncLevel1) - average(IncLevel2)

Motoufiq commented 1 week ago

@EricKutschera thank you very much.