Your submission: human_sim_long_short 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 20706
Number of known genes detected 20597
Number of transcripts detected 47545
Number of transcripts associated to a known gene 47047
Number of unique SJ detected 191123
Absolute value Relative value (%)
Novel SJ 7298 0.04
Non-canonical SJ 6479 0.03

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 37409 -
Reference Match 32759 87.57
5’ reference supported (transcript) 34830 93.11
3’ reference supported (transcript) 34579 92.43
5’ reference supported (gene) 35888 95.93
3’ reference supported (gene) 36035 96.33
Supported Reference Transcript Model (SRTM) 34766 92.93
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1523 -
5’ reference supported (transcript) 343 22.52
3’ reference supported (transcript) 469 30.79
5’ and 3’ reference supported (gene) 229 15.04
5’ reference supported (gene) 572 572
3’ reference supported (gene) 747 49.05
Supported Reference Transcript Model (SRTM) 229 15.04
Reference redundancy Level 1.05 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 3763 -
5’ and 3’ reference supported (gene) 2288 60.8
5’ reference supported (gene) 3075 81.72
3’ reference supported (gene) 2739 72.79
Intron retention incidence 892 23.7

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 4352 -
5’ and 3’ reference supported (gene) 335 7.7
5’ reference supported (gene) 3962 91.04
3’ reference supported (gene) 428 9.83
Non-canonical SJ incidence 3747 86.1
Full Illumina SJ support 4352 100
RT-switching incidence 541 12.43

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) 30768
Number of transcripts associated to TP (Reference Match) 30795
Partial True Positive detections (PTP) 5273
Number of transcripts associated to PTP 5430
False Negative (FN) 12612
False Positive (FP) 11320
Sensitivity 0.64
Precision 0.65
Non Redundant Precision 0.65
Positive Detection Rate 0.74
False Discovery Rate 0.35
False Detection Rate 0.24
Redundancy 1.02

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 41964
True Positive detections (TP) 30020
Number of transcripts associated to TP (Reference Match) 30044
Partial True Positive detections (PTP) 3600
Number of transcripts associated to PTP 3690
False Negative (FN) 8795
False Positive (FP) 13811
Sensitivity 0.72
Positive Detection Rate 0.79
Redundancy 1.02

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 28414
True Positive detections (TP) 22130
Number of transcripts associated to TP (Reference Match) 22148
Partial True Positive detections (PTP) 2050
Number of transcripts associated to PTP 2123
False Negative (FN) 4634
False Positive (FP) 23274
Sensitivity 0.78
Positive Detection Rate 0.84
Redundancy 1.02

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 16196
True Positive detections (TP) 13450
Number of transcripts associated to TP (Reference Match) 13463
Partial True Positive detections (PTP) 968
Number of transcripts associated to PTP 1019
False Negative (FN) 2080
False Positive (FP) 33063
Sensitivity 0.83
Positive Detection Rate 0.87
Redundancy 1.03

Evaluation of novelty

Value
Number of isoforms simulated 6228
True Positive detections (TP) 748
Number of transcripts associated to TP (Reference Match) 751
Partial True Positive detections (PTP) 1673
Number of transcripts associated to PTP 1740
False Negative (FN) 3817
False Positive (FP) 45054
Sensitivity 0.12
Positive Detection Rate 0.39
Redundancy 1.03