Rmats image

[alquamalok22]

Hi Eric

I am doing the rmats sashimi plot but was unable to get the splice junctions. If i am using A3SS.txt file so how to chose the coordinates. Can you please help..

chr	strand	longExonStart_0base	longExonEnd	shortES	shortEE	flankingES	flankingEE
chr6	+	10724575	10725037	10724960	10725037	10723124	10723241

[EricKutschera]

It looks like you are running rmats2sashimiplot with coordinates and a gff3 using -c. In that case only the junctions in the gff3 will be shown. If you run with --event-type and -e using the rmats output file then it would show the junctions for the event: #57

Also it looks like the coordinate range you are plotting does not include the flanking exon (10723124, 10723241), but it's just the long exon (10724575, 10725037)