Your submission: H1_mix_captrap_ont on ONT data

Background

Challenge 1 is evaluated according to four criteria:

  1. Broad GENCODE Annotation
  2. Subset of manually curated loci selected by GENCODE
  3. SIRV Lexogen Set 4
  4. Simulated data.

The LRGASP uses SQANTI categories to define evaluating features and metrics for Challenge 1.

LRGASP Challenge 1 Definitions:

This document shows the performance of your pipeline for criteria 1. and 3. Critical data for evaluation according to 2. and 4. will be made available after the closure of the challenge, and therefore pre-evaluation reports cannot be provided. Note you’re your criterion 1 metrics reported here have been calculated using GENCODE human v38 and mouse M27 releases while the final evaluation will use human v39 and mouse M28 to be released after completing of the challenge.

Evaluation of detected transcripts for Challenge 1

Here, SIRVs are not taken into account for none of the metrics.

Global overview

Value
Number of genes detected 7638
Number of known genes detected 7593
Number of transcripts detected 25555
Number of transcripts associated to a known gene 23839
Number of unique SJ detected 68753
Absolute value Relative value (%)
Novel SJ 6046 0.09
Non-canonical SJ 16446 0.24

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 13241 -
Reference Match 11683 88.23
5’ reference supported (transcript) 12660 95.61
3’ reference supported (transcript) 11952 90.27
5’ reference supported (gene) 13049 98.55
3’ reference supported (gene) 12722 96.08
5’ CAGE supported 9320 70.39
3’ polyA supported 12204 92.17
Supported Reference Transcript Model (SRTM) 13007 98.23
Intra-priming 325 2.45
Reference redundancy Level 1.05 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1090 -
5’ reference supported (transcript) 421 38.62
3’ reference supported (transcript) 392 35.96
5’ and 3’ reference supported (gene) 229 21.01
5’ reference supported (gene) 617 617
3’ reference supported (gene) 592 54.31
5’ CAGE supported 522 47.89
3’ polyA supported 902 82.75
Supported Reference Transcript Model (SRTM) 495 45.41
Intra-priming 118 10.83
Reference redundancy Level 1.06 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 4221 -
5’ and 3’ reference supported (gene) 1121 26.56
5’ reference supported (gene) 1404 33.26
3’ reference supported (gene) 1254 29.71
5’ CAGE supported 1155 27.36
3’ polyA supported 1509 35.75
Supported Novel Transcript Model (SNTM) 1080 25.59
Intra-priming 55 1.3
Intron retention incidence 583 13.81

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 5287 -
5’ and 3’ reference supported (gene) 3494 66.09
5’ reference supported (gene) 4137 78.25
3’ reference supported (gene) 3921 74.16
5’ CAGE supported 3829 72.42
3’ polyA supported 4588 86.78
Supported Novel Transcript Model (SNTM) 784 14.83
Non-canonical SJ incidence 1312 24.82
Full Illumina SJ support 950 17.97
Intra-priming 94 1.78
RT-switching incidence 215 4.07

Evaluation of Spike-Ins (SIRVs)

The following metrics and definitions apply to SIRV transcripts:

ATENTION If in this chunk of the evaluation all the results are 0, please, check if the reference genome and/or transcriptome used for building your transcript-model contain information about spike-ins.

Value
SIRV transcripts 113
True Positive detections (TP) 62
SIRV transcripts associated to TP (Reference Match) 62
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 1
False Negative (FN) 22
False Positive (FP) 50
Sensitivity 0.74
Precision 0.55
Non Redundant Precision 0.55
Positive Detection Rate 0.74
False Discovery Rate 0.44
False Detection Rate 0.44
Redundancy 1.02