Multiple events with similar locations

[ebonner303]

Salutations, I am running RMATS on some pateint data (150 bp PE reads) and I am noticing that I am getting multiple events with very similar locations (a variant is a few base pairs longer or shorter than another). My guess is that this is likely noise from the sequencer and these are not true variants. I try to filter my results downstream by setting a threshold for read number, but I am still running into this issue, is there a way to set stricter settings when running RMATS to condense these down and improve downstream analysis?

[EricKutschera]

You can run with --individual-counts and the output will include columns showing the read count for each junction in the event. The events with similar coordinates should differ for at least 1 junction. Then you could try filtering by the individual junction counts