RI.MATS.JCEC — strand and 5′/3′ orientation for RI introns

[Adi Gershon]

In the RI.MATS.JCEC file, are upstreamES/EE and downstreamES/EE reported in genomic order regardless of strand, with the retained intron being [upstreamEE, downstreamES)? If so, for negative-strand events, does the “upstream exon” correspond to the 3′ side of the intron and the “downstream exon” to the 5′ side (i.e., should I reverse negative-strand events to plot profiles in 5′→3′ transcript direction)? Also, please confirm coordinates are 0-based start, 1-based exclusive end.

[kutsc...@gmail.com]

Coordinates are reported in genomic order regardless of strand. The retained intron is upstreamEE to downstreamES. For negative strand events the upstream exon is 3' and the downstream exon is 5'. The coordinates for start columns are 0-based first position of the exon (riExonStart_0base, upstreamES, downstreamES). The coordinates for end columns are 1-based last position of the exon (riExonEnd, upstreamEE, downstreamEE)

https://github.com/Xinglab/rmats-turbo/issues/158

https://github.com/Xinglab/rmats-turbo/issues/479#issuecomment-2734045669

Eric