Stringtie3 exon number of negative strand is in wrong order

[SophieEhres]

Hello,

While running Stringtie3, I noticed the exon numbers were always ordered according to their position on the + strand even if the transcript is on the - strand:

chr16 StringTie transcript 86474525 86508879 1000 - . gene_id "FENDRR"; transcript_id "FENDRR.14"; longcov "37.000000"; cov "58.697742"; FPKM "4.363515"; TPM "8.534764";
chr16 StringTie exon 86474525 86477199 1000 - . gene_id "FENDRR"; transcript_id "FENDRR.14"; exon_number "1"; cov "54.251400";
chr16 StringTie exon 86478701 86478756 1000 - . gene_id "FENDRR"; transcript_id "FENDRR.14"; exon_number "2"; cov "86.046165";
chr16 StringTie exon 86490264 86491004 1000 - . gene_id "FENDRR"; transcript_id "FENDRR.14"; exon_number "3"; cov "78.124825";
chr16 StringTie exon 86508655 86508879 1000 - . gene_id "FENDRR"; transcript_id "FENDRR.14"; exon_number "5"; cov "64.897110";

Some tools I use rely on exon number and I have to reorder all the negative strand exons. It would be nice to have the Stringtie output be correctly ordered.

Thanks!

Sophie