Your submission: Simulated_mouse 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 15327
Number of known genes detected 13950
Number of transcripts detected 25874
Number of transcripts associated to a known gene 24363
Number of unique SJ detected 143337
Absolute value Relative value (%)
Novel SJ 349 0
Non-canonical SJ 529 0

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 23815 -
Reference Match 23672 99.4
5’ reference supported (transcript) 23728 99.63
3’ reference supported (transcript) 23716 99.58
5’ reference supported (gene) 23757 99.76
3’ reference supported (gene) 23753 99.74
Supported Reference Transcript Model (SRTM) 23716 99.58
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 209 -
5’ reference supported (transcript) 33 15.79
3’ reference supported (transcript) 156 74.64
5’ and 3’ reference supported (gene) 37 17.7
5’ reference supported (gene) 64 64
3’ reference supported (gene) 179 85.65
Supported Reference Transcript Model (SRTM) 37 17.7
Reference redundancy Level 1 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 168 -
5’ and 3’ reference supported (gene) 132 78.57
5’ reference supported (gene) 136 80.95
3’ reference supported (gene) 152 90.48
Intron retention incidence 24 14.29

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 171 -
5’ and 3’ reference supported (gene) 145 84.8
5’ reference supported (gene) 152 88.89
3’ reference supported (gene) 150 87.72
Non-canonical SJ incidence 128 74.85
Full Illumina SJ support 171 100
RT-switching incidence 43 25.15

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) 23628
Number of transcripts associated to TP (Reference Match) 23635
Partial True Positive detections (PTP) 254
Number of transcripts associated to PTP 257
False Negative (FN) 3388
False Positive (FP) 1982
Sensitivity 0.87
Precision 0.91
Non Redundant Precision 0.91
Positive Detection Rate 0.88
False Discovery Rate 0.09
False Detection Rate 0.08
Redundancy 1.01

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 20152
True Positive detections (TP) 17999
Number of transcripts associated to TP (Reference Match) 18006
Partial True Positive detections (PTP) 187
Number of transcripts associated to PTP 190
False Negative (FN) 2072
False Positive (FP) 7678
Sensitivity 0.89
Positive Detection Rate 0.9
Redundancy 1.01

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 15608
True Positive detections (TP) 14581
Number of transcripts associated to TP (Reference Match) 14585
Partial True Positive detections (PTP) 108
Number of transcripts associated to PTP 110
False Negative (FN) 983
False Positive (FP) 11179
Sensitivity 0.93
Positive Detection Rate 0.94
Redundancy 1

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 9428
True Positive detections (TP) 9105
Number of transcripts associated to TP (Reference Match) 9106
Partial True Positive detections (PTP) 45
Number of transcripts associated to PTP 47
False Negative (FN) 308
False Positive (FP) 16721
Sensitivity 0.97
Positive Detection Rate 0.97
Redundancy 1

Evaluation of novelty

Value
Number of isoforms simulated 7000
True Positive detections (TP) 5629
Number of transcripts associated to TP (Reference Match) 5629
Partial True Positive detections (PTP) 67
Number of transcripts associated to PTP 67
False Negative (FN) 1316
False Positive (FP) 20178
Sensitivity 0.8
Positive Detection Rate 0.81
Redundancy 1