LiftOn
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Kuanhao-Chao
LiftOff generates better BUSCO scores than LiftOn
Hi there,
I was testing LiftOff and LiftOn to see which one is "best" for genome annotation. I was looking at some RefSeq genomes, lifting the brown-headed cowbird and red-winged blackbird onto the bronzed cowbird. Interestingly, in both cases LiftOff created better BUSCO scores and LiftOn also generated some weird features where the end coordinate of the feature was earlier than the start coordinate. Although LiftOff generated better BUSCO scores, GFFCompare suggested that the LiftOn genome had more matching transcripts, but the precision was a tad lower. As a result, I feel I trust LiftOff more as an annotation tool and wanted to bring these results to your attention.
Here is my BUSCO score for LiftOff, brown-headed cowbird on bronzed cowbird:
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|Results from dataset passeriformes_odb10 |
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|C:93.6%[S:60.2%,D:33.4%],F:1.2%,M:5.2%,n:10844 |
|10148 Complete BUSCOs (C) |
|6526 Complete and single-copy BUSCOs (S) |
|3622 Complete and duplicated BUSCOs (D) |
|127 Fragmented BUSCOs (F) |
|569 Missing BUSCOs (M) |
|10844 Total BUSCO groups searched |
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And here is GFFCompare, when comparing this brown-headed cowbird LiftOff annotation to the RefSeq annotation:
#-----------------| Sensitivity | Precision |
Base level: 89.2 | 84.4 |
Exon level: 85.6 | 87.7 |
Intron level: 90.0 | 92.2 |
Intron chain level: 59.9 | 58.1 |
Transcript level: 60.4 | 58.7 |
Locus level: 71.2 | 74.4 |
Matching intron chains: 17652
Matching transcripts: 18650
Matching loci: 13081
Missed exons: 15337/199727 ( 7.7%)
Novel exons: 10077/195294 ( 5.2%)
Missed introns: 11294/180584 ( 6.3%)
Novel introns: 5639/176399 ( 3.2%)
Missed loci: 1914/18371 ( 10.4%)
Novel loci: 1166/17582 ( 6.6%)
Here is BUSCO for LiftOn, brown-headed cowbird on bronzed cowbird:
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|Results from dataset passeriformes_odb10 |
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|C:71.1%[S:47.5%,D:23.6%],F:0.4%,M:28.5%,n:10844 |
|7708 Complete BUSCOs (C) |
|5150 Complete and single-copy BUSCOs (S) |
|2558 Complete and duplicated BUSCOs (D) |
|46 Fragmented BUSCOs (F) |
|3090 Missing BUSCOs (M) |
|10844 Total BUSCO groups searched |
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GFFCompare for LiftOn brown-headed cowbird compared to RefSeq:
#-----------------| Sensitivity | Precision |
Base level: 89.5 | 84.2 |
Exon level: 86.0 | 87.2 |
Intron level: 90.4 | 91.7 |
Intron chain level: 60.2 | 57.9 |
Transcript level: 60.8 | 58.4 |
Locus level: 71.8 | 73.5 |
Matching intron chains: 17721
Matching transcripts: 18765
Matching loci: 13198
Missed exons: 14512/199727 ( 7.3%)
Novel exons: 11255/197273 ( 5.7%)
Missed introns: 10598/180584 ( 5.9%)
Novel introns: 6515/177980 ( 3.7%)
Missed loci: 1760/18371 ( 9.6%)
Novel loci: 1388/17956 ( 7.7%)
BUSCO for LiftOff of red-winged blackbird on bronzed cowbird:
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|Results from dataset passeriformes_odb10 |
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|C:97.3%[S:69.3%,D:28.0%],F:0.4%,M:2.3%,n:10844 |
|10551 Complete BUSCOs (C) |
|7510 Complete and single-copy BUSCOs (S) |
|3041 Complete and duplicated BUSCOs (D) |
|39 Fragmented BUSCOs (F) |
|254 Missing BUSCOs (M) |
|10844 Total BUSCO groups searched |
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GFFCompare of LiftOff red-winged blackbird compared to RefSeq annotation:
#-----------------| Sensitivity | Precision |
Base level: 76.9 | 90.0 |
Exon level: 82.0 | 85.5 |
Intron level: 87.0 | 90.2 |
Intron chain level: 44.3 | 46.0 |
Transcript level: 45.3 | 46.8 |
Locus level: 62.1 | 66.1 |
Matching intron chains: 13052
Matching transcripts: 13987
Matching loci: 11409
Missed exons: 19028/199727 ( 9.5%)
Novel exons: 10245/191797 ( 5.3%)
Missed introns: 12796/180584 ( 7.1%)
Novel introns: 5096/174094 ( 2.9%)
Missed loci: 2101/18371 ( 11.4%)
Novel loci: 923/17215 ( 5.4%)
BUSCO of LiftOn red-winged blackbird onto bronzed cowbird:
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|Results from dataset passeriformes_odb10 |
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|C:61.3%[S:44.0%,D:17.3%],F:0.4%,M:38.3%,n:10844 |
|6649 Complete BUSCOs (C) |
|4768 Complete and single-copy BUSCOs (S) |
|1881 Complete and duplicated BUSCOs (D) |
|44 Fragmented BUSCOs (F) |
|4151 Missing BUSCOs (M) |
|10844 Total BUSCO groups searched |
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GFFCompare of LiftOn red-winged blackbird compared to RefSeq annotation:
#-----------------| Sensitivity | Precision |
Base level: 77.2 | 89.9 |
Exon level: 82.4 | 85.3 |
Intron level: 87.4 | 90.1 |
Intron chain level: 44.9 | 46.2 |
Transcript level: 45.9 | 47.0 |
Locus level: 63.0 | 66.1 |
Matching intron chains: 13209
Matching transcripts: 14176
Matching loci: 11571
Missed exons: 18326/199727 ( 9.2%)
Novel exons: 10918/193146 ( 5.7%)
Missed introns: 12242/180584 ( 6.8%)
Novel introns: 5639/175141 ( 3.2%)
Missed loci: 1977/18371 ( 10.8%)
Novel loci: 1050/17477 ( 6.0%)
