Your submission: human_simulation_cDNA_PacBio on PacBio 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 20329
Number of known genes detected 20124
Number of transcripts detected 46964
Number of transcripts associated to a known gene 46742
Number of unique SJ detected 183311
Absolute value Relative value (%)
Novel SJ 826 0
Non-canonical SJ 516 0

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 42807 -
Reference Match 42647 99.63
5’ reference supported (transcript) 42724 99.81
3’ reference supported (transcript) 42686 99.72
5’ reference supported (gene) 42761 99.89
3’ reference supported (gene) 42745 99.86
Supported Reference Transcript Model (SRTM) 42717 99.79
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2899 -
5’ reference supported (transcript) 194 6.69
3’ reference supported (transcript) 2492 85.96
5’ and 3’ reference supported (gene) 492 16.97
5’ reference supported (gene) 647 647
3’ reference supported (gene) 2714 93.62
Supported Reference Transcript Model (SRTM) 492 16.97
Reference redundancy Level 1.03 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 563 -
5’ and 3’ reference supported (gene) 520 92.36
5’ reference supported (gene) 533 94.67
3’ reference supported (gene) 546 96.98
Intron retention incidence 90 15.99

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 473 -
5’ and 3’ reference supported (gene) 401 84.78
5’ reference supported (gene) 433 91.54
3’ reference supported (gene) 427 90.27
Non-canonical SJ incidence 184 38.9
Full Illumina SJ support 473 100
RT-switching incidence 49 10.36

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) 42475
Number of transcripts associated to TP (Reference Match) 42501
Partial True Positive detections (PTP) 2843
Number of transcripts associated to PTP 2944
False Negative (FN) 5171
False Positive (FP) 1519
Sensitivity 0.88
Precision 0.9
Non Redundant Precision 0.9
Positive Detection Rate 0.89
False Discovery Rate 0.09
False Detection Rate 0.03
Redundancy 1.06

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 41964
True Positive detections (TP) 38769
Number of transcripts associated to TP (Reference Match) 38795
Partial True Positive detections (PTP) 2344
Number of transcripts associated to PTP 2436
False Negative (FN) 2921
False Positive (FP) 5733
Sensitivity 0.92
Positive Detection Rate 0.93
Redundancy 1.06

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 28414
True Positive detections (TP) 26823
Number of transcripts associated to TP (Reference Match) 26845
Partial True Positive detections (PTP) 2006
Number of transcripts associated to PTP 2083
False Negative (FN) 1436
False Positive (FP) 18036
Sensitivity 0.94
Positive Detection Rate 0.95
Redundancy 1.07

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 16196
True Positive detections (TP) 15418
Number of transcripts associated to TP (Reference Match) 15436
Partial True Positive detections (PTP) 1237
Number of transcripts associated to PTP 1287
False Negative (FN) 718
False Positive (FP) 30241
Sensitivity 0.95
Positive Detection Rate 0.96
Redundancy 1.08

Evaluation of novelty

Value
Number of isoforms simulated 6228
True Positive detections (TP) 3706
Number of transcripts associated to TP (Reference Match) 3706
Partial True Positive detections (PTP) 499
Number of transcripts associated to PTP 508
False Negative (FN) 2250
False Positive (FP) 42750
Sensitivity 0.6
Positive Detection Rate 0.64
Redundancy 1.06