Your submission: mouse_sim_cdna_pacbio_ls on PacBio+Illumina 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 13946
Number of known genes detected 13916
Number of transcripts detected 25135
Number of transcripts associated to a known gene 25100
Number of unique SJ detected 141806
Absolute value Relative value (%)
Novel SJ 360 0
Non-canonical SJ 421 0

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 24113 -
Reference Match 23900 99.12
5’ reference supported (transcript) 23968 99.4
3’ reference supported (transcript) 23952 99.33
5’ reference supported (gene) 24052 99.75
3’ reference supported (gene) 24068 99.81
Supported Reference Transcript Model (SRTM) 24016 99.6
Reference redundancy Level 1.01 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 429 -
5’ reference supported (transcript) 60 13.99
3’ reference supported (transcript) 177 41.26
5’ and 3’ reference supported (gene) 171 39.86
5’ reference supported (gene) 229 229
3’ reference supported (gene) 345 80.42
Supported Reference Transcript Model (SRTM) 171 39.86
Reference redundancy Level 1.01 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 319 -
5’ and 3’ reference supported (gene) 274 85.89
5’ reference supported (gene) 285 89.34
3’ reference supported (gene) 303 94.98
Intron retention incidence 11 3.45

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 239 -
5’ and 3’ reference supported (gene) 139 58.16
5’ reference supported (gene) 171 71.55
3’ reference supported (gene) 187 78.24
Non-canonical SJ incidence 18 7.53
Full Illumina SJ support 239 100
RT-switching incidence 13 5.44

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) 22960
Number of transcripts associated to TP (Reference Match) 23009
Partial True Positive detections (PTP) 434
Number of transcripts associated to PTP 446
False Negative (FN) 3998
False Positive (FP) 1680
Sensitivity 0.85
Precision 0.92
Non Redundant Precision 0.91
Positive Detection Rate 0.85
False Discovery Rate 0.08
False Detection Rate 0.07
Redundancy 1.01

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 20152
True Positive detections (TP) 20057
Number of transcripts associated to TP (Reference Match) 20106
Partial True Positive detections (PTP) 216
Number of transcripts associated to PTP 219
False Negative (FN) 90
False Positive (FP) 4810
Sensitivity 1
Positive Detection Rate 1
Redundancy 1.01

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 15608
True Positive detections (TP) 15572
Number of transcripts associated to TP (Reference Match) 15611
Partial True Positive detections (PTP) 140
Number of transcripts associated to PTP 143
False Negative (FN) 36
False Positive (FP) 9381
Sensitivity 1
Positive Detection Rate 1
Redundancy 1.01

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 9428
True Positive detections (TP) 9416
Number of transcripts associated to TP (Reference Match) 9430
Partial True Positive detections (PTP) 65
Number of transcripts associated to PTP 68
False Negative (FN) 12
False Positive (FP) 15637
Sensitivity 1
Positive Detection Rate 1
Redundancy 1.01

Evaluation of novelty

Value
Number of isoforms simulated 7000
True Positive detections (TP) 2903
Number of transcripts associated to TP (Reference Match) 2903
Partial True Positive detections (PTP) 218
Number of transcripts associated to PTP 227
False Negative (FN) 3908
False Positive (FP) 22005
Sensitivity 0.41
Positive Detection Rate 0.44
Redundancy 1.01