Cannot process two consecutive (annotated) microexons

[therealgenna]

It looks like when there are two annotated microexons one next to the other the splice junctions are not created and the microexons get ignored (and not reported anywhere in the final output even if they have support.)

Here is an example snapshot of my analysis. I took the junction names from the fasta headers in the Round1 and Round2 directories. Here we have two 9-nt exons one after the other, and they are lost.

"missing" means missing splice junction to the next exon (>=30bp), not missing exon

The 3 columns are annotated exons from gtf (with their length), splice junctions constructed in Round1, and splice junctions constructed in Round2