qqwang-berkeley
AS junction co-ordinates are sometimes wrong.
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
I am more than happy to provide additional files to help pinpoint this discrepancy.
AS_event_ID as described by JUM:
Illustration in IGV. green represents co-ordinates matching with that from STAR. red represents discrepancy.
edit: i forgot to mention the set of transcript annotations below the reference is a reconstructed transcriptome from my data. it is not the reference annotation.
Snippet of SJ.out.tab
It seems that the .bam junctions view in IGV has minused all co-ordinates by 1 across the board. I initially thought it had something to do with co-ordinates taken as starting from 1 compared to 0. However, the additional short-fall in red highlighted co-ordinate in IGV cannot be explained.
This may be due to difference in sam (1 indexed)/bed(0 indexed) format indexing. For more information, I found this discussion: https://www.biostars.org/p/84686/.
Do you know if it has been fixed?
