Your submission: human_sim_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 19883
Number of known genes detected 19859
Number of transcripts detected 43539
Number of transcripts associated to a known gene 43514
Number of unique SJ detected 181185
Absolute value Relative value (%)
Novel SJ 474 0.00
Non-canonical SJ 1078 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 42350 -
Reference Match 42056 99.31
5’ reference supported (transcript) 42172 99.58
3’ reference supported (transcript) 42132 99.49
5’ reference supported (gene) 42281 99.84
3’ reference supported (gene) 42299 99.88
Supported Reference Transcript Model (SRTM) 42239 99.74
Reference redundancy Level 1.01 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 566 -
5’ reference supported (transcript) 65 11.48
3’ reference supported (transcript) 263 46.47
5’ and 3’ reference supported (gene) 255 45.05
5’ reference supported (gene) 305 305
3’ reference supported (gene) 494 87.28
Supported Reference Transcript Model (SRTM) 255 45.05
Reference redundancy Level 1 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 273 -
5’ and 3’ reference supported (gene) 219 80.22
5’ reference supported (gene) 237 86.81
3’ reference supported (gene) 250 91.58
Intron retention incidence 30 10.99

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 325 -
5’ and 3’ reference supported (gene) 201 61.85
5’ reference supported (gene) 236 72.62
3’ reference supported (gene) 268 82.46
Non-canonical SJ incidence 3 0.92
Full Illumina SJ support 325 100
RT-switching incidence 10 3.08

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) 41339
Number of transcripts associated to TP (Reference Match) 41411
Partial True Positive detections (PTP) 649
Number of transcripts associated to PTP 654
False Negative (FN) 6635
False Positive (FP) 1474
Sensitivity 0.86
Precision 0.95
Non Redundant Precision 0.95
Positive Detection Rate 0.86
False Discovery Rate 0.05
False Detection Rate 0.03
Redundancy 1.01

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 41964
True Positive detections (TP) 39821
Number of transcripts associated to TP (Reference Match) 39893
Partial True Positive detections (PTP) 464
Number of transcripts associated to PTP 465
False Negative (FN) 2099
False Positive (FP) 3181
Sensitivity 0.95
Positive Detection Rate 0.95
Redundancy 1.01

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 28414
True Positive detections (TP) 28301
Number of transcripts associated to TP (Reference Match) 28372
Partial True Positive detections (PTP) 367
Number of transcripts associated to PTP 368
False Negative (FN) 109
False Positive (FP) 14799
Sensitivity 1
Positive Detection Rate 1
Redundancy 1.02

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 16196
True Positive detections (TP) 16162
Number of transcripts associated to TP (Reference Match) 16209
Partial True Positive detections (PTP) 182
Number of transcripts associated to PTP 183
False Negative (FN) 34
False Positive (FP) 27147
Sensitivity 1
Positive Detection Rate 1
Redundancy 1.01

Evaluation of novelty

Value
Number of isoforms simulated 6228
True Positive detections (TP) 1518
Number of transcripts associated to TP (Reference Match) 1518
Partial True Positive detections (PTP) 185
Number of transcripts associated to PTP 189
False Negative (FN) 4536
False Positive (FP) 41832
Sensitivity 0.24
Positive Detection Rate 0.27
Redundancy 1.01