Your submission: mouse_simulation_pb 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 41429
Number of known genes detected 15102
Number of transcripts detected 158641
Number of transcripts associated to a known gene 46330
Number of unique SJ detected 498755
Absolute value Relative value (%)
Novel SJ 320553 0.64
Non-canonical SJ 333508 0.67

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 23026 -
Reference Match 22277 96.75
5’ reference supported (transcript) 22569 98.02
3’ reference supported (transcript) 22614 98.21
5’ reference supported (gene) 22675 98.48
3’ reference supported (gene) 22721 98.68
Supported Reference Transcript Model (SRTM) 22443 97.47
Reference redundancy Level 1.01 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1424 -
5’ reference supported (transcript) 263 18.47
3’ reference supported (transcript) 1062 74.58
5’ and 3’ reference supported (gene) 158 11.1
5’ reference supported (gene) 424 424
3’ reference supported (gene) 1118 78.51
Supported Reference Transcript Model (SRTM) 158 11.1
Reference redundancy Level 1.04 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 232 -
5’ and 3’ reference supported (gene) 124 53.45
5’ reference supported (gene) 139 59.91
3’ reference supported (gene) 140 60.34
Intron retention incidence 42 18.1

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 21648 -
5’ and 3’ reference supported (gene) 1807 8.35
5’ reference supported (gene) 2917 13.47
3’ reference supported (gene) 2096 9.68
Non-canonical SJ incidence 20816 96.16
Full Illumina SJ support 21648 100
RT-switching incidence 1367 6.31

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 27152
True Positive detections (TP) 22241
Number of transcripts associated to TP (Reference Match) 22244
Partial True Positive detections (PTP) 1885
Number of transcripts associated to PTP 1979
False Negative (FN) 4257
False Positive (FP) 134418
Sensitivity 0.82
Precision 0.14
Non Redundant Precision 0.14
Positive Detection Rate 0.84
False Discovery Rate 0.86
False Detection Rate 0.85
Redundancy 1.06

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 20152
True Positive detections (TP) 16023
Number of transcripts associated to TP (Reference Match) 16023
Partial True Positive detections (PTP) 1158
Number of transcripts associated to PTP 1200
False Negative (FN) 3598
False Positive (FP) 141418
Sensitivity 0.8
Positive Detection Rate 0.82
Redundancy 1.04

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 15608
True Positive detections (TP) 13539
Number of transcripts associated to TP (Reference Match) 13539
Partial True Positive detections (PTP) 845
Number of transcripts associated to PTP 880
False Negative (FN) 1804
False Positive (FP) 144222
Sensitivity 0.87
Positive Detection Rate 0.88
Redundancy 1.04

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 9428
True Positive detections (TP) 8771
Number of transcripts associated to TP (Reference Match) 8771
Partial True Positive detections (PTP) 493
Number of transcripts associated to PTP 515
False Negative (FN) 591
False Positive (FP) 149355
Sensitivity 0.93
Positive Detection Rate 0.94
Redundancy 1.05

Evaluation of novelty

Value
Number of isoforms simulated 7000
True Positive detections (TP) 6218
Number of transcripts associated to TP (Reference Match) 6221
Partial True Positive detections (PTP) 727
Number of transcripts associated to PTP 779
False Negative (FN) 659
False Positive (FP) 151641
Sensitivity 0.89
Positive Detection Rate 0.91
Redundancy 1.1