Your submission: human_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 20911
Number of known genes detected 20759
Number of transcripts detected 46766
Number of transcripts associated to a known gene 46574
Number of unique SJ detected 183739
Absolute value Relative value (%)
Novel SJ 1296 0.01
Non-canonical SJ 1640 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 39988 -
Reference Match 39203 98.04
5’ reference supported (transcript) 39297 98.27
3’ reference supported (transcript) 39769 99.45
5’ reference supported (gene) 39451 98.66
3’ reference supported (gene) 39944 99.89
Supported Reference Transcript Model (SRTM) 39416 98.57
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 5625 -
5’ reference supported (transcript) 136 2.42
3’ reference supported (transcript) 5276 93.8
5’ and 3’ reference supported (gene) 676 12.02
5’ reference supported (gene) 780 780
3’ reference supported (gene) 5500 97.78
Supported Reference Transcript Model (SRTM) 676 12.02
Reference redundancy Level 1.04 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 523 -
5’ and 3’ reference supported (gene) 304 58.13
5’ reference supported (gene) 327 62.52
3’ reference supported (gene) 487 93.12
Intron retention incidence 75 14.34

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 438 -
5’ and 3’ reference supported (gene) 356 81.28
5’ reference supported (gene) 372 84.93
3’ reference supported (gene) 389 88.81
Non-canonical SJ incidence 297 67.81
Full Illumina SJ support 438 100
RT-switching incidence 69 15.75

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) 39165
Number of transcripts associated to TP (Reference Match) 39167
Partial True Positive detections (PTP) 5902
Number of transcripts associated to PTP 6124
False Negative (FN) 7964
False Positive (FP) 1475
Sensitivity 0.81
Precision 0.84
Non Redundant Precision 0.84
Positive Detection Rate 0.83
False Discovery Rate 0.16
False Detection Rate 0.03
Redundancy 1.13

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 41964
True Positive detections (TP) 33946
Number of transcripts associated to TP (Reference Match) 33946
Partial True Positive detections (PTP) 5030
Number of transcripts associated to PTP 5225
False Negative (FN) 7017
False Positive (FP) 7595
Sensitivity 0.81
Positive Detection Rate 0.83
Redundancy 1.12

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 28414
True Positive detections (TP) 25257
Number of transcripts associated to TP (Reference Match) 25257
Partial True Positive detections (PTP) 3895
Number of transcripts associated to PTP 4075
False Negative (FN) 2759
False Positive (FP) 17434
Sensitivity 0.89
Positive Detection Rate 0.9
Redundancy 1.14

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 16196
True Positive detections (TP) 15301
Number of transcripts associated to TP (Reference Match) 15301
Partial True Positive detections (PTP) 2620
Number of transcripts associated to PTP 2756
False Negative (FN) 708
False Positive (FP) 28709
Sensitivity 0.94
Positive Detection Rate 0.96
Redundancy 1.17

Evaluation of novelty

Value
Number of isoforms simulated 6228
True Positive detections (TP) 5219
Number of transcripts associated to TP (Reference Match) 5221
Partial True Positive detections (PTP) 872
Number of transcripts associated to PTP 899
False Negative (FN) 947
False Positive (FP) 40646
Sensitivity 0.84
Positive Detection Rate 0.85
Redundancy 1.16