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 20837
Number of known genes detected 20837
Number of transcripts detected 44161
Number of transcripts associated to a known gene 44150
Number of unique SJ detected 188304
Absolute value Relative value (%)
Novel SJ 261 0.00
Non-canonical SJ 1047 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 43581 -
Reference Match 43120 98.94
5’ reference supported (transcript) 43340 99.45
3’ reference supported (transcript) 43188 99.1
5’ reference supported (gene) 43473 99.75
3’ reference supported (gene) 43276 99.3
Supported Reference Transcript Model (SRTM) 43238 99.21
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 97 -
5’ reference supported (transcript) 37 38.14
3’ reference supported (transcript) 24 24.74
5’ and 3’ reference supported (gene) 59 60.82
5’ reference supported (gene) 77 77
3’ reference supported (gene) 75 77.32
Supported Reference Transcript Model (SRTM) 59 60.82
Reference redundancy Level 1 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 302 -
5’ and 3’ reference supported (gene) 270 89.4
5’ reference supported (gene) 290 96.03
3’ reference supported (gene) 276 91.39
Intron retention incidence 35 11.59

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 170 -
5’ and 3’ reference supported (gene) 101 59.41
5’ reference supported (gene) 146 85.88
3’ reference supported (gene) 114 67.06
Non-canonical SJ incidence 60 35.29
Full Illumina SJ support 170 100
RT-switching incidence 42 24.71

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) 42625
Number of transcripts associated to TP (Reference Match) 42645
Partial True Positive detections (PTP) 517
Number of transcripts associated to PTP 518
False Negative (FN) 5091
False Positive (FP) 998
Sensitivity 0.88
Precision 0.97
Non Redundant Precision 0.97
Positive Detection Rate 0.89
False Discovery Rate 0.03
False Detection Rate 0.02
Redundancy 1

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 41964
True Positive detections (TP) 39590
Number of transcripts associated to TP (Reference Match) 39595
Partial True Positive detections (PTP) 380
Number of transcripts associated to PTP 380
False Negative (FN) 2021
False Positive (FP) 4186
Sensitivity 0.94
Positive Detection Rate 0.95
Redundancy 1

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 28414
True Positive detections (TP) 26710
Number of transcripts associated to TP (Reference Match) 26713
Partial True Positive detections (PTP) 258
Number of transcripts associated to PTP 258
False Negative (FN) 1464
False Positive (FP) 17190
Sensitivity 0.94
Positive Detection Rate 0.95
Redundancy 1

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 16196
True Positive detections (TP) 15131
Number of transcripts associated to TP (Reference Match) 15131
Partial True Positive detections (PTP) 137
Number of transcripts associated to PTP 137
False Negative (FN) 943
False Positive (FP) 28893
Sensitivity 0.93
Positive Detection Rate 0.94
Redundancy 1

Evaluation of novelty

Value
Number of isoforms simulated 6228
True Positive detections (TP) 3035
Number of transcripts associated to TP (Reference Match) 3050
Partial True Positive detections (PTP) 137
Number of transcripts associated to PTP 138
False Negative (FN) 3070
False Positive (FP) 40973
Sensitivity 0.49
Positive Detection Rate 0.51
Redundancy 1.01