Your submission: human_sim_cdna_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. sim 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 4. 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

Global overview

Value
Number of genes detected 16824
Number of known genes detected 16822
Number of transcripts detected 25556
Number of transcripts associated to a known gene 25521
Number of unique SJ detected 108817
Absolute value Relative value (%)
Novel SJ 641 0.01
Non-canonical SJ 577 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 23756 -
Reference Match 23331 98.21
5’ reference supported (transcript) 23537 99.08
3’ reference supported (transcript) 23430 98.63
5’ reference supported (gene) 23633 99.48
3’ reference supported (gene) 23482 98.85
Supported Reference Transcript Model (SRTM) 23418 98.58
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1123 -
5’ reference supported (transcript) 206 18.34
3’ reference supported (transcript) 243 21.64
5’ and 3’ reference supported (gene) 40 3.56
5’ reference supported (gene) 286 286
3’ reference supported (gene) 316 28.14
Supported Reference Transcript Model (SRTM) 40 3.56
Reference redundancy Level 1.05 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 237 -
5’ and 3’ reference supported (gene) 83 35.02
5’ reference supported (gene) 154 64.98
3’ reference supported (gene) 119 50.21
Intron retention incidence 51 21.52

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 405 -
5’ and 3’ reference supported (gene) 95 23.46
5’ reference supported (gene) 218 53.83
3’ reference supported (gene) 164 40.49
Non-canonical SJ incidence 7 1.73
Full Illumina SJ support 405 100
RT-switching incidence 39 9.63

Evaluation of Simulation

Simulated transcripts were grouped according to different thresholds and attributes, so metrics were calculated regarding to these ground truth setttings. These sets of ground truth transcripts are:

The following metrics and definitions apply to simulated transcripts.

Evaluation of all simulated transcripts

Value
Number of isoforms simulated 48192
True Positive detections (TP) 22561
Number of transcripts associated to TP (Reference Match) 22566
Partial True Positive detections (PTP) 1361
Number of transcripts associated to PTP 1418
False Negative (FN) 24531
False Positive (FP) 1572
Sensitivity 0.47
Precision 0.88
Non Redundant Precision 0.88
Positive Detection Rate 0.49
False Discovery Rate 0.11
False Detection Rate 0.06
Redundancy 1.01

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 41964
True Positive detections (TP) 21979
Number of transcripts associated to TP (Reference Match) 21982
Partial True Positive detections (PTP) 847
Number of transcripts associated to PTP 888
False Negative (FN) 19388
False Positive (FP) 2686
Sensitivity 0.52
Positive Detection Rate 0.54
Redundancy 1.01

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 28414
True Positive detections (TP) 15269
Number of transcripts associated to TP (Reference Match) 15271
Partial True Positive detections (PTP) 681
Number of transcripts associated to PTP 720
False Negative (FN) 12683
False Positive (FP) 9565
Sensitivity 0.54
Positive Detection Rate 0.55
Redundancy 1.02

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 16196
True Positive detections (TP) 9001
Number of transcripts associated to TP (Reference Match) 9002
Partial True Positive detections (PTP) 429
Number of transcripts associated to PTP 459
False Negative (FN) 6919
False Positive (FP) 16095
Sensitivity 0.56
Positive Detection Rate 0.57
Redundancy 1.02

Evaluation of novelty

Value
Number of isoforms simulated 6228
True Positive detections (TP) 582
Number of transcripts associated to TP (Reference Match) 584
Partial True Positive detections (PTP) 514
Number of transcripts associated to PTP 530
False Negative (FN) 5143
False Positive (FP) 24442
Sensitivity 0.09
Positive Detection Rate 0.17
Redundancy 1.03