exon length is ZERO! about stringtie

[gpertea]

No -- could you provide an example output line please? I'm assuming such exons are not given as reference annotation to StringTie..

[yji1983]

1 StringTie exon 22175136 22175287 1000 - . gene_id "MSTRG.391"; transcript_id "MSTRG.391.8"; exon_number "21";
1 StringTie exon 22175386 22175524 1000 - . gene_id "MSTRG.391"; transcript_id "MSTRG.391.8"; exon_number "22";
1 StringTie exon 22176534 22176685 1000 - . gene_id "MSTRG.391"; transcript_id "MSTRG.391.8"; exon_number "23";
1 StringTie exon 22176856 22176991 1000 - . gene_id "MSTRG.391"; transcript_id "MSTRG.391.8"; exon_number "24";
1 StringTie exon 22178039 22178083 1000 - . gene_id "MSTRG.391"; transcript_id "MSTRG.391.8"; exon_number "25";
1 StringTie exon 22179457 22179563 1000 - . gene_id "MSTRG.391"; transcript_id "MSTRG.391.8"; exon_number "26";
1 StringTie exon 22180301 22180301 1000 - . gene_id "MSTRG.391"; transcript_id "MSTRG.391.8"; exon_number "27";

[gpertea]

That's length 1 (not 0), which is theoretically possible (microexon) but could also be an artifact caused by spurious alignments.
I couldn't tell -- is that the last exon of that transcript ? Also, what was the aligner used?
It would be very helpful if you could provide us with the .BAM alignments in that region - is that a possibility? Also, if any reference annotation was used, I am curious if there was a micro-exon annotated at that coordinate already..
Thank you!