Hello,
I have the following problem. I first used TopHat to map my RNA-Seq reads to the hg19 reference. After that I used TopHat's accepted_hits.bam file to search for alternative splicing events with MISO. I did everything like it was described in the MISO manual and everything was fine (No errors, no warnings). The MISO-summary contains tab-seprated values and most of them are either self-explanatory or further specified in the MISO manual. However the last two columns don't make any sense to me. The first line of exon-skipping events is given below showing only the first column and the last two columns:
event_name ... mRNA_starts mRNA_ends
chr15:99276430:99277179:+@chr15:99277759:99277983:+@chr15:99282239:99282513:+ ... 101458907 101464990
The event_name always consists of an exon triplet, whereby two of them are constitutive exons and the one in the middle is an alternative exon. What I don't understand is, why mRNA_starts column has a higher coordinate than any of the exons? Can somebody explain this value to me? The MISO-documentation does not help me at all.
Best regards
