Your submission: iso_detect_ref_spectra_human_simulation 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 34162
Number of known genes detected 22295
Number of transcripts detected 88816
Number of transcripts associated to a known gene 66845
Number of unique SJ detected 329914
Absolute value Relative value (%)
Novel SJ 5095 0.02
Non-canonical SJ 140489 0.43

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 45797 -
Reference Match 44606 97.4
5’ reference supported (transcript) 44824 97.88
3’ reference supported (transcript) 45379 99.09
5’ reference supported (gene) 45084 98.44
3’ reference supported (gene) 45725 99.84
Supported Reference Transcript Model (SRTM) 45043 98.35
Reference redundancy Level 1.02 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 9417 -
5’ reference supported (transcript) 255 2.71
3’ reference supported (transcript) 8612 91.45
5’ and 3’ reference supported (gene) 1371 14.56
5’ reference supported (gene) 1557 1557
3’ reference supported (gene) 9179 97.47
Supported Reference Transcript Model (SRTM) 1371 14.56
Reference redundancy Level 1.11 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 6522 -
5’ and 3’ reference supported (gene) 1620 24.84
5’ reference supported (gene) 1822 27.94
3’ reference supported (gene) 2175 33.35
Intron retention incidence 1349 20.68

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 5109 -
5’ and 3’ reference supported (gene) 4088 80.02
5’ reference supported (gene) 4255 83.28
3’ reference supported (gene) 4826 94.46
Non-canonical SJ incidence 3321 65
Full Illumina SJ support 5109 100
RT-switching incidence 934 18.28

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) 44292
Number of transcripts associated to TP (Reference Match) 44580
Partial True Positive detections (PTP) 8858
Number of transcripts associated to PTP 10180
False Negative (FN) 3124
False Positive (FP) 34056
Sensitivity 0.92
Precision 0.5
Non Redundant Precision 0.5
Positive Detection Rate 0.94
False Discovery Rate 0.48
False Detection Rate 0.38
Redundancy 1.22

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 41964
True Positive detections (TP) 39078
Number of transcripts associated to TP (Reference Match) 39112
Partial True Positive detections (PTP) 7276
Number of transcripts associated to PTP 8054
False Negative (FN) 2232
False Positive (FP) 41650
Sensitivity 0.93
Positive Detection Rate 0.95
Redundancy 1.19

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 28414
True Positive detections (TP) 26607
Number of transcripts associated to TP (Reference Match) 26615
Partial True Positive detections (PTP) 5509
Number of transcripts associated to PTP 6172
False Negative (FN) 1370
False Positive (FP) 56029
Sensitivity 0.94
Positive Detection Rate 0.95
Redundancy 1.21

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 16196
True Positive detections (TP) 15250
Number of transcripts associated to TP (Reference Match) 15252
Partial True Positive detections (PTP) 3303
Number of transcripts associated to PTP 3754
False Negative (FN) 683
False Positive (FP) 69810
Sensitivity 0.94
Positive Detection Rate 0.96
Redundancy 1.23

Evaluation of novelty

Value
Number of isoforms simulated 6228
True Positive detections (TP) 5214
Number of transcripts associated to TP (Reference Match) 5468
Partial True Positive detections (PTP) 1582
Number of transcripts associated to PTP 2126
False Negative (FN) 892
False Positive (FP) 81222
Sensitivity 0.84
Positive Detection Rate 0.86
Redundancy 1.42