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gpertea / stringtie

Transcript assembly and quantification for RNA-Seq
MIT License
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which output file contains identified novel exons in stringtie/2.2.1 ? #435

Open erajshafiq opened 4 months ago

erajshafiq commented 4 months ago

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