Your submission: mouse_simulation_PacBio_cDNA_long 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 14355
Number of known genes detected 14162
Number of transcripts detected 28245
Number of transcripts associated to a known gene 27998
Number of unique SJ detected 144146
Absolute value Relative value (%)
Novel SJ 1280 0.01
Non-canonical SJ 1568 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 23865 -
Reference Match 23470 98.34
5’ reference supported (transcript) 23600 98.89
3’ reference supported (transcript) 23616 98.96
5’ reference supported (gene) 23673 99.2
3’ reference supported (gene) 23761 99.56
Supported Reference Transcript Model (SRTM) 23605 98.91
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 3576 -
5’ reference supported (transcript) 116 3.24
3’ reference supported (transcript) 3274 91.55
5’ and 3’ reference supported (gene) 317 8.86
5’ reference supported (gene) 426 426
3’ reference supported (gene) 3447 96.39
Supported Reference Transcript Model (SRTM) 317 8.86
Reference redundancy Level 1.05 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 293 -
5’ and 3’ reference supported (gene) 196 66.89
5’ reference supported (gene) 202 68.94
3’ reference supported (gene) 285 97.27
Intron retention incidence 26 8.87

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 264 -
5’ and 3’ reference supported (gene) 195 73.86
5’ reference supported (gene) 205 77.65
3’ reference supported (gene) 211 79.92
Non-canonical SJ incidence 166 62.88
Full Illumina SJ support 264 100
RT-switching incidence 42 15.91

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) 23385
Number of transcripts associated to TP (Reference Match) 23386
Partial True Positive detections (PTP) 3412
Number of transcripts associated to PTP 3575
False Negative (FN) 3451
False Positive (FP) 1284
Sensitivity 0.86
Precision 0.83
Non Redundant Precision 0.83
Positive Detection Rate 0.87
False Discovery Rate 0.17
False Detection Rate 0.05
Redundancy 1.14

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 20152
True Positive detections (TP) 17360
Number of transcripts associated to TP (Reference Match) 17361
Partial True Positive detections (PTP) 2217
Number of transcripts associated to PTP 2313
False Negative (FN) 2538
False Positive (FP) 8571
Sensitivity 0.86
Positive Detection Rate 0.87
Redundancy 1.12

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 15608
True Positive detections (TP) 14127
Number of transcripts associated to TP (Reference Match) 14128
Partial True Positive detections (PTP) 1809
Number of transcripts associated to PTP 1884
False Negative (FN) 1323
False Positive (FP) 12233
Sensitivity 0.91
Positive Detection Rate 0.92
Redundancy 1.12

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 9428
True Positive detections (TP) 9047
Number of transcripts associated to TP (Reference Match) 9048
Partial True Positive detections (PTP) 1172
Number of transcripts associated to PTP 1215
False Negative (FN) 317
False Positive (FP) 17982
Sensitivity 0.96
Positive Detection Rate 0.97
Redundancy 1.13

Evaluation of novelty

Value
Number of isoforms simulated 7000
True Positive detections (TP) 6025
Number of transcripts associated to TP (Reference Match) 6025
Partial True Positive detections (PTP) 1195
Number of transcripts associated to PTP 1262
False Negative (FN) 913
False Positive (FP) 20958
Sensitivity 0.86
Positive Detection Rate 0.87
Redundancy 1.2