Entering edit mode
6.9 years ago
amy16
▴
40
Hi all, Below is the output from gffcompare of assembled transcripts from my RNA-seq experiment with the reference genome annotation. I am concerned about the low precision values. Do I have to rerun my assembly?
Query mRNAs : 74136 in 32930 loci (63219 multi-exon transcripts)
(13176 multi-transcript loci, ~2.3 transcripts per locus)
Reference mRNAs : 28269 in 28269 loci (20429 multi-exon)
Super-loci w/ reference transcripts: 27162
-----------------| Sensitivity | Precision |
Base level: 100.0 | 65.6 |
Exon level: 100.0 | 58.8 |
Intron level: 100.0 | 72.2 |
Intron chain level: 100.0 | 32.3 | Transcript level: 100.0 | 38.1 | Locus level: 100.0 | 83.2 |
Matching intron chains: 20429
Matching transcripts: 28269
Matching loci: 28269
Missed exons: 0/139417 ( 0.0%)
Novel exons: 44143/240416 ( 18.4%)
Missed introns: 0/111148 ( 0.0%)
Novel introns: 22898/153871 ( 14.9%)
Missed loci: 0/28269 ( 0.0%)
Novel loci: 5421/32930 ( 16.5%)
Total union super-loci across all input datasets: 32930 74136 out of 74136 consensus transcripts written in prrmerg07.annotated.gtf (0 discarded as redundant)
Thanks
Sorry, I know it has been a long time since this was posted, but I also have low precision values and I am wondering if you found out why that is?