Inconsistent column numbers in the "*JCEC.txt" output

[XMTian]

Dear authors,

Thank you for developing this useful tool.

I'm using the output "*JCEC.txt" to get significant DS events, however, I found the output file has inconsistent column numbers, including both 23 and 25, as follows.

I'm bringing this to your attention and hope you will correct it.

Best wishes,
Xiaomeng

[EricKutschera]

There are different event types which have different columns. All the event types start with the columns:

ID, GeneID, geneSymbol, chr, strand

All of the event types end with the columns:

ID, IJC_SAMPLE_1, SJC_SAMPLE_1, IJC_SAMPLE_2, SJC_SAMPLE_2, IncFormLen, SkipFormLen, PValue, FDR, IncLevel1, IncLevel2, IncLevelDifference

The middle columns differ by event type. For SE the columns are:

exonStart_0base, exonEnd, upstreamES, upstreamEE, downstreamES, downstreamEE

For A5SS and A3SS the columns are:

longExonStart_0base, longExonEnd, shortES, shortEE, flankingES, flankingEE

For MXE:

1stExonStart_0base, 1stExonEnd, 2ndExonStart_0base, 2ndExonEnd, upstreamES, upstreamEE, downstreamES, downstreamEE

For RI:

riExonStart_0base, riExonEnd, upstreamES, upstreamEE, downstreamES, downstreamEE

This post shows the event specific columns in a diagram: #158 (comment)

If you run with --individual-counts there will be additional event specific columns. These columns are listed in the README: https://github.com/Xinglab/rmats-turbo/tree/v4.3.0?tab=readme-ov-file#output