Your submission: iso_detect_ref_spectra_mouse_simulation 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 26036
Number of known genes detected 15507
Number of transcripts detected 63659
Number of transcripts associated to a known gene 43502
Number of unique SJ detected 273722
Absolute value Relative value (%)
Novel SJ 5828 0.02
Non-canonical SJ 125473 0.46

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 26971 -
Reference Match 25522 94.63
5’ reference supported (transcript) 25752 95.48
3’ reference supported (transcript) 26541 98.41
5’ reference supported (gene) 25935 96.16
3’ reference supported (gene) 26800 99.37
Supported Reference Transcript Model (SRTM) 25835 95.79
Reference redundancy Level 1.05 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 6052 -
5’ reference supported (transcript) 313 5.17
3’ reference supported (transcript) 5320 87.9
5’ and 3’ reference supported (gene) 738 12.19
5’ reference supported (gene) 1030 1030
3’ reference supported (gene) 5697 94.13
Supported Reference Transcript Model (SRTM) 738 12.19
Reference redundancy Level 1.13 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 4675 -
5’ and 3’ reference supported (gene) 1255 26.84
5’ reference supported (gene) 1332 28.49
3’ reference supported (gene) 1576 33.71
Intron retention incidence 542 11.59

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 5804 -
5’ and 3’ reference supported (gene) 4420 76.15
5’ reference supported (gene) 4716 81.25
3’ reference supported (gene) 5282 91.01
Non-canonical SJ incidence 3331 57.39
Full Illumina SJ support 5804 100
RT-switching incidence 944 16.26

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) 25109
Number of transcripts associated to TP (Reference Match) 25461
Partial True Positive detections (PTP) 5522
Number of transcripts associated to PTP 7006
False Negative (FN) 1650
False Positive (FP) 31192
Sensitivity 0.92
Precision 0.4
Non Redundant Precision 0.39
Positive Detection Rate 0.94
False Discovery Rate 0.58
False Detection Rate 0.49
Redundancy 1.27

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 20152
True Positive detections (TP) 18979
Number of transcripts associated to TP (Reference Match) 18981
Partial True Positive detections (PTP) 3303
Number of transcripts associated to PTP 3674
False Negative (FN) 890
False Positive (FP) 41004
Sensitivity 0.94
Positive Detection Rate 0.96
Redundancy 1.18

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 15608
True Positive detections (TP) 14774
Number of transcripts associated to TP (Reference Match) 14776
Partial True Positive detections (PTP) 2586
Number of transcripts associated to PTP 2892
False Negative (FN) 628
False Positive (FP) 45991
Sensitivity 0.95
Positive Detection Rate 0.96
Redundancy 1.18

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 9428
True Positive detections (TP) 9031
Number of transcripts associated to TP (Reference Match) 9033
Partial True Positive detections (PTP) 1510
Number of transcripts associated to PTP 1694
False Negative (FN) 290
False Positive (FP) 52932
Sensitivity 0.96
Positive Detection Rate 0.97
Redundancy 1.17

Evaluation of novelty

Value
Number of isoforms simulated 7000
True Positive detections (TP) 6130
Number of transcripts associated to TP (Reference Match) 6480
Partial True Positive detections (PTP) 2219
Number of transcripts associated to PTP 3332
False Negative (FN) 760
False Positive (FP) 53847
Sensitivity 0.88
Positive Detection Rate 0.89
Redundancy 1.57