which output file contains identified novel exons in stringtie/2.2.1 ?

[erajshafiq]

Hi - I am running stringtie after STAR (BAM file includes the XS tag):

stringtie -o string_tie_test.gtf --rf -G ./Homo_sapiens.GRCh38.95.gtf -p 10 test.bam

And then running gffcompare to compare the results

According to *.stats file there are around 14% novel exons. But I can only find labels for transcripts in the *annotated.gtf file but no labels in the exons to see if they are novel or not.

Can you please help me figure out which output file contains the identified novel exons?

Thanks, Eraj