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 20136
Number of known genes detected 20082
Number of transcripts detected 50074
Number of transcripts associated to a known gene 49946
Number of unique SJ detected 187789
Absolute value Relative value (%)
Novel SJ 4670 0.02
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 43284 -
Reference Match 42502 98.19
5’ reference supported (transcript) 42870 99.04
3’ reference supported (transcript) 42862 99.03
5’ reference supported (gene) 43071 99.51
3’ reference supported (gene) 43247 99.91
Supported Reference Transcript Model (SRTM) 43042 99.44
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 529 -
5’ reference supported (transcript) 54 10.21
3’ reference supported (transcript) 425 80.34
5’ and 3’ reference supported (gene) 127 24.01
5’ reference supported (gene) 158 158
3’ reference supported (gene) 488 92.25
Supported Reference Transcript Model (SRTM) 127 24.01
Reference redundancy Level 1 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 920 -
5’ and 3’ reference supported (gene) 635 69.02
5’ reference supported (gene) 640 69.57
3’ reference supported (gene) 909 98.8
Intron retention incidence 121 13.15

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 5213 -
5’ and 3’ reference supported (gene) 5001 95.93
5’ reference supported (gene) 5039 96.66
3’ reference supported (gene) 5164 99.06
Non-canonical SJ incidence 0 0
Full Illumina SJ support 5213 100
RT-switching incidence 316 6.06

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) 42473
Number of transcripts associated to TP (Reference Match) 42474
Partial True Positive detections (PTP) 1179
Number of transcripts associated to PTP 1182
False Negative (FN) 4632
False Positive (FP) 6418
Sensitivity 0.88
Precision 0.85
Non Redundant Precision 0.85
Positive Detection Rate 0.9
False Discovery Rate 0.15
False Detection Rate 0.13
Redundancy 1

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 41964
True Positive detections (TP) 37154
Number of transcripts associated to TP (Reference Match) 37154
Partial True Positive detections (PTP) 1056
Number of transcripts associated to PTP 1059
False Negative (FN) 3831
False Positive (FP) 11861
Sensitivity 0.89
Positive Detection Rate 0.91
Redundancy 1

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 28414
True Positive detections (TP) 26022
Number of transcripts associated to TP (Reference Match) 26022
Partial True Positive detections (PTP) 477
Number of transcripts associated to PTP 479
False Negative (FN) 1976
False Positive (FP) 23573
Sensitivity 0.92
Positive Detection Rate 0.93
Redundancy 1

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 16196
True Positive detections (TP) 14959
Number of transcripts associated to TP (Reference Match) 14959
Partial True Positive detections (PTP) 240
Number of transcripts associated to PTP 241
False Negative (FN) 1027
False Positive (FP) 34874
Sensitivity 0.92
Positive Detection Rate 0.94
Redundancy 1

Evaluation of novelty

Value
Number of isoforms simulated 6228
True Positive detections (TP) 5319
Number of transcripts associated to TP (Reference Match) 5320
Partial True Positive detections (PTP) 123
Number of transcripts associated to PTP 123
False Negative (FN) 801
False Positive (FP) 44631
Sensitivity 0.85
Positive Detection Rate 0.87
Redundancy 1