Your submission: mouse_simulation_dRNA_ONT on ONT 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 9063
Number of known genes detected 8908
Number of transcripts detected 12067
Number of transcripts associated to a known gene 11879
Number of unique SJ detected 41825
Absolute value Relative value (%)
Novel SJ 245 0.01
Non-canonical SJ 18 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 9676 -
Reference Match 9587 99.08
5’ reference supported (transcript) 9622 99.44
3’ reference supported (transcript) 9604 99.26
5’ reference supported (gene) 9635 99.58
3’ reference supported (gene) 9612 99.34
Supported Reference Transcript Model (SRTM) 9597 99.18
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1788 -
5’ reference supported (transcript) 360 20.13
3’ reference supported (transcript) 351 19.63
5’ and 3’ reference supported (gene) 36 2.01
5’ reference supported (gene) 466 466
3’ reference supported (gene) 418 23.38
Supported Reference Transcript Model (SRTM) 36 2.01
Reference redundancy Level 1.12 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 339 -
5’ and 3’ reference supported (gene) 49 14.45
5’ reference supported (gene) 123 36.28
3’ reference supported (gene) 126 37.17
Intron retention incidence 168 49.56

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 76 -
5’ and 3’ reference supported (gene) 28 36.84
5’ reference supported (gene) 42 55.26
3’ reference supported (gene) 37 48.68
Non-canonical SJ incidence 3 3.95
Full Illumina SJ support 76 100
RT-switching incidence 2 2.63

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) 8262
Number of transcripts associated to TP (Reference Match) 8275
Partial True Positive detections (PTP) 1462
Number of transcripts associated to PTP 1620
False Negative (FN) 17713
False Positive (FP) 2172
Sensitivity 0.3
Precision 0.69
Non Redundant Precision 0.68
Positive Detection Rate 0.35
False Discovery Rate 0.3
False Detection Rate 0.18
Redundancy 1.05

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 20152
True Positive detections (TP) 8198
Number of transcripts associated to TP (Reference Match) 8211
Partial True Positive detections (PTP) 993
Number of transcripts associated to PTP 1101
False Negative (FN) 11245
False Positive (FP) 2755
Sensitivity 0.41
Positive Detection Rate 0.44
Redundancy 1.05

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 15608
True Positive detections (TP) 6554
Number of transcripts associated to TP (Reference Match) 6564
Partial True Positive detections (PTP) 865
Number of transcripts associated to PTP 963
False Negative (FN) 8435
False Positive (FP) 4540
Sensitivity 0.42
Positive Detection Rate 0.46
Redundancy 1.05

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 9428
True Positive detections (TP) 4431
Number of transcripts associated to TP (Reference Match) 4439
Partial True Positive detections (PTP) 606
Number of transcripts associated to PTP 686
False Negative (FN) 4561
False Positive (FP) 6942
Sensitivity 0.47
Positive Detection Rate 0.52
Redundancy 1.05

Evaluation of novelty

Value
Number of isoforms simulated 7000
True Positive detections (TP) 64
Number of transcripts associated to TP (Reference Match) 64
Partial True Positive detections (PTP) 469
Number of transcripts associated to PTP 519
False Negative (FN) 6468
False Positive (FP) 11484
Sensitivity 0.01
Positive Detection Rate 0.08
Redundancy 1.1