Your submission: human_sim_cdna_ont_ls on ONT+Illumina 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 18242
Number of known genes detected 16070
Number of transcripts detected 48566
Number of transcripts associated to a known gene 44575
Number of unique SJ detected 92393
Absolute value Relative value (%)
Novel SJ 1639 0.02
Non-canonical SJ 358 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 15132 -
Reference Match 7859 51.94
5’ reference supported (transcript) 12050 79.63
3’ reference supported (transcript) 8257 54.57
5’ reference supported (gene) 12896 85.22
3’ reference supported (gene) 8781 58.03
Supported Reference Transcript Model (SRTM) 8429 55.7
Reference redundancy Level 1.1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 25815 -
5’ reference supported (transcript) 3724 14.43
3’ reference supported (transcript) 2177 8.43
5’ and 3’ reference supported (gene) 126 0.49
5’ reference supported (gene) 4887 4887
3’ reference supported (gene) 2931 11.35
Supported Reference Transcript Model (SRTM) 126 0.49
Reference redundancy Level 1.73 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 2347 -
5’ and 3’ reference supported (gene) 215 9.16
5’ reference supported (gene) 695 29.61
3’ reference supported (gene) 527 22.45
Intron retention incidence 64 2.73

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 1281 -
5’ and 3’ reference supported (gene) 240 18.74
5’ reference supported (gene) 595 46.45
3’ reference supported (gene) 427 33.33
Non-canonical SJ incidence 17 1.33
Full Illumina SJ support 1281 100
RT-switching incidence 60 4.68

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) 6967
Number of transcripts associated to TP (Reference Match) 6989
Partial True Positive detections (PTP) 18158
Number of transcripts associated to PTP 30793
False Negative (FN) 23850
False Positive (FP) 10784
Sensitivity 0.14
Precision 0.14
Non Redundant Precision 0.14
Positive Detection Rate 0.51
False Discovery Rate 0.6
False Detection Rate 0.22
Redundancy 1.55

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 41964
True Positive detections (TP) 6607
Number of transcripts associated to TP (Reference Match) 6629
Partial True Positive detections (PTP) 15289
Number of transcripts associated to PTP 26232
False Negative (FN) 20833
False Positive (FP) 15705
Sensitivity 0.16
Positive Detection Rate 0.5
Redundancy 1.56

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 28414
True Positive detections (TP) 4328
Number of transcripts associated to TP (Reference Match) 4345
Partial True Positive detections (PTP) 13547
Number of transcripts associated to PTP 24073
False Negative (FN) 11194
False Positive (FP) 20148
Sensitivity 0.15
Positive Detection Rate 0.61
Redundancy 1.65

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 16196
True Positive detections (TP) 2414
Number of transcripts associated to TP (Reference Match) 2426
Partial True Positive detections (PTP) 9806
Number of transcripts associated to PTP 19112
False Negative (FN) 4442
False Positive (FP) 27028
Sensitivity 0.15
Positive Detection Rate 0.73
Redundancy 1.83

Evaluation of novelty

Value
Number of isoforms simulated 6228
True Positive detections (TP) 360
Number of transcripts associated to TP (Reference Match) 360
Partial True Positive detections (PTP) 2869
Number of transcripts associated to PTP 4561
False Negative (FN) 3017
False Positive (FP) 43645
Sensitivity 0.06
Positive Detection Rate 0.52
Redundancy 1.53