Is there a way to annotate the splice junctions output from tophat/STAR output?
What I mean by annotate is can I know if it was involved in an alternative splicing event say skipped exon, MXE or retained intron...?
I did some research looks like rMATS does it but we do not have access to the data all we have is output from tophat(.bed file) and STAR(SJ.out) files
Data available: Splice junction files from star and tophat2 for some reason they deleted the bams in the same directory (from what i know they purged all files with size greater than something)
Species: human aligned to GRCh37(ensembl).
Goal :
Annotate splice junctions based on event it is involved an event skipped exon, MXE or A3ss or A5ss.
I did some more research and saw that ucsc table browser has UCSC Alt events as an option the data looks like this
#bin chrom chromStart chromEnd name score strand
0 chr1 67108547 67109226 atacIntron 0 +
22 chr1 111148925 111149075 altPromoter 0 -
35 chr1 220046661 220292759 strangeSplice 0 +
73 chr1 917423 917573 altPromoter 0 -
75 chr1 2489907 2491261 retainedIntron 0 +
93 chr1 21494532 21496156 strangeSplice 0 -
95 chr1 23720526 23724037 atacIntron 0 -
100 chr1 28835417 28837404 bleedingExon 0 +
153 chr1 84259617 84379035 strangeSplice 0 -
Not sure how they curate this.
