Your submission: mouse_sim_drna_ont_ls on ONT+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 10811
Number of known genes detected 10709
Number of transcripts detected 20527
Number of transcripts associated to a known gene 20342
Number of unique SJ detected 57469
Absolute value Relative value (%)
Novel SJ 595 0.01
Non-canonical SJ 148 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 7793 -
Reference Match 4968 63.75
5’ reference supported (transcript) 6713 86.14
3’ reference supported (transcript) 5091 65.33
5’ reference supported (gene) 7093 91.02
3’ reference supported (gene) 5256 67.45
Supported Reference Transcript Model (SRTM) 5138 65.93
Reference redundancy Level 1.06 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 11242 -
5’ reference supported (transcript) 1326 11.8
3’ reference supported (transcript) 1301 11.57
5’ and 3’ reference supported (gene) 62 0.55
5’ reference supported (gene) 1781 1781
3’ reference supported (gene) 1730 15.39
Supported Reference Transcript Model (SRTM) 62 0.55
Reference redundancy Level 1.4 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 869 -
5’ and 3’ reference supported (gene) 70 8.06
5’ reference supported (gene) 169 19.45
3’ reference supported (gene) 235 27.04
Intron retention incidence 27 3.11

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 438 -
5’ and 3’ reference supported (gene) 78 17.81
5’ reference supported (gene) 165 37.67
3’ reference supported (gene) 155 35.39
Non-canonical SJ incidence 10 2.28
Full Illumina SJ support 438 100
RT-switching incidence 14 3.2

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) 4003
Number of transcripts associated to TP (Reference Match) 4017
Partial True Positive detections (PTP) 9064
Number of transcripts associated to PTP 12602
False Negative (FN) 14509
False Positive (FP) 3908
Sensitivity 0.15
Precision 0.2
Non Redundant Precision 0.2
Positive Detection Rate 0.47
False Discovery Rate 0.63
False Detection Rate 0.19
Redundancy 1.31

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 20152
True Positive detections (TP) 3807
Number of transcripts associated to TP (Reference Match) 3821
Partial True Positive detections (PTP) 7032
Number of transcripts associated to PTP 9915
False Negative (FN) 9725
False Positive (FP) 6791
Sensitivity 0.19
Positive Detection Rate 0.52
Redundancy 1.32

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 15608
True Positive detections (TP) 3113
Number of transcripts associated to TP (Reference Match) 3124
Partial True Positive detections (PTP) 6554
Number of transcripts associated to PTP 9352
False Negative (FN) 6308
False Positive (FP) 8051
Sensitivity 0.2
Positive Detection Rate 0.6
Redundancy 1.34

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 9428
True Positive detections (TP) 2129
Number of transcripts associated to TP (Reference Match) 2136
Partial True Positive detections (PTP) 5050
Number of transcripts associated to PTP 7552
False Negative (FN) 2533
False Positive (FP) 10839
Sensitivity 0.23
Positive Detection Rate 0.73
Redundancy 1.41

Evaluation of novelty

Value
Number of isoforms simulated 7000
True Positive detections (TP) 196
Number of transcripts associated to TP (Reference Match) 196
Partial True Positive detections (PTP) 2032
Number of transcripts associated to PTP 2687
False Negative (FN) 4784
False Positive (FP) 17644
Sensitivity 0.03
Positive Detection Rate 0.32
Redundancy 1.3