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 8785
Number of known genes detected 8311
Number of transcripts detected 24229
Number of transcripts associated to a known gene 20702
Number of unique SJ detected 69005
Absolute value Relative value (%)
Novel SJ 4149 0.06
Non-canonical SJ 16524 0.24

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 5529 -
Reference Match 4860 87.9
5’ reference supported (transcript) 5153 93.2
3’ reference supported (transcript) 4943 89.4
5’ reference supported (gene) 5252 94.99
3’ reference supported (gene) 5015 90.7
Supported Reference Transcript Model (SRTM) 4932 89.2
Reference redundancy Level 1.04 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 7425 -
5’ reference supported (transcript) 419 5.64
3’ reference supported (transcript) 467 6.29
5’ and 3’ reference supported (gene) 27 0.36
5’ reference supported (gene) 640 640
3’ reference supported (gene) 658 8.86
Supported Reference Transcript Model (SRTM) 27 0.36
Reference redundancy Level 1.74 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 3911 -
5’ and 3’ reference supported (gene) 109 2.79
5’ reference supported (gene) 264 6.75
3’ reference supported (gene) 231 5.91
Intron retention incidence 369 9.43

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 3837 -
5’ and 3’ reference supported (gene) 1098 28.62
5’ reference supported (gene) 1526 39.77
3’ reference supported (gene) 1827 47.62
Non-canonical SJ incidence 992 25.85
Full Illumina SJ support 3837 100
RT-switching incidence 185 4.82

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) 4520
Number of transcripts associated to TP (Reference Match) 4531
Partial True Positive detections (PTP) 4406
Number of transcripts associated to PTP 7582
False Negative (FN) 39466
False Positive (FP) 12116
Sensitivity 0.09
Precision 0.19
Non Redundant Precision 0.19
Positive Detection Rate 0.18
False Discovery Rate 0.68
False Detection Rate 0.5
Redundancy 1.39

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 41964
True Positive detections (TP) 4477
Number of transcripts associated to TP (Reference Match) 4488
Partial True Positive detections (PTP) 3353
Number of transcripts associated to PTP 5575
False Negative (FN) 34332
False Positive (FP) 14166
Sensitivity 0.11
Positive Detection Rate 0.18
Redundancy 1.32

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 28414
True Positive detections (TP) 3347
Number of transcripts associated to TP (Reference Match) 3356
Partial True Positive detections (PTP) 3051
Number of transcripts associated to PTP 5122
False Negative (FN) 22173
False Positive (FP) 15751
Sensitivity 0.12
Positive Detection Rate 0.22
Redundancy 1.36

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 16196
True Positive detections (TP) 1992
Number of transcripts associated to TP (Reference Match) 1996
Partial True Positive detections (PTP) 2430
Number of transcripts associated to PTP 4180
False Negative (FN) 11884
False Positive (FP) 18053
Sensitivity 0.12
Positive Detection Rate 0.27
Redundancy 1.43

Evaluation of novelty

Value
Number of isoforms simulated 6228
True Positive detections (TP) 43
Number of transcripts associated to TP (Reference Match) 43
Partial True Positive detections (PTP) 1053
Number of transcripts associated to PTP 2007
False Negative (FN) 5134
False Positive (FP) 22179
Sensitivity 0.01
Positive Detection Rate 0.18
Redundancy 1.87