AS junction co-ordinates are sometimes wrong.

[angel-bee2018]

Hi,

I've been using the time-series pipeline of JUM and noticed that the junction co-ordinates are consistently lower compared to when viewed in IGV as well as the reference annotation. This problem seems to begin all the way from the JUM_temp_A step, with the UNION_junc_coor co-ordinates already different to those in the SJ.out.tab file from STAR.

Upon further exploration, I noticed that the co-ordinates are usually 1 less than expected. Under certain circumstances (mostly in cassette exon calls), some co-ordinates may be correct and some may be short between sub-junctions with in the same AS junction.

I hope that this issue can be looked into. Best wishes