How to statistics the novel transcripts about gffcompare HOT 2 CLOSED

Hello Trandamere,
I am also new to RNA-SEQ analysis. I also followed this same protocol for my dataset. And i am having some problem for identifying novel transcripts and genes from the below gffcompare ".stats" file

i was running the following command $ gffcompare –r chrX_data/genes/chrX.gtf –G –o merged stringtie_merged.gtf. and i got the result file as
= Summary for dataset: stringtie_merged.gtf
Query mRNAs : 253181 in 70635 loci (216728 multi-exon transcripts)
(23264 multi-transcript loci, ~3.6 transcripts per locus)
Reference mRNAs : 216257 in 60158 loci (189357 multi-exon)
Super-loci w/ reference transcripts: 51791
-----------------| Sensitivity | Precision |

Base level:   100.0     |    93.0    |
Exon level:    99.9     |    93.6    |

Intron level: 99.4 | 94.0 |

Intron chain level: 99.7 | 87.1 | Transcript level: 99.8 | 85.2 | Locus level: 100.0 | 84.4 |

Matching intron chains: 188838
Matching transcripts: 215729
Matching loci: 60158

  Missed exons:       0/623537  (  0.0%)
   Novel exons:   23741/674273  (  3.5%)
Missed introns:    2160/383827  (  0.6%)
 Novel introns:    4747/405880  (  1.2%)
   Missed loci:       0/60158   (  0.0%)
    Novel loci:   10239/70635   ( 14.5%)

Total union super-loci across all input datasets: 70632 253181 out of 253181 consensus transcripts written in merged.annotated.gtf (0 discarded as redundant).

from this result where i can find the novel genes and transcripts?

from gffcompare.

Closing this as it is generally addressed in the answer to #24 and the online documentation.

from gffcompare.