Your submission: mouse_sim_drna_ont on ONT 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 11157
Number of known genes detected 11157
Number of transcripts detected 15190
Number of transcripts associated to a known gene 15184
Number of unique SJ detected 85793
Absolute value Relative value (%)
Novel SJ 312 0
Non-canonical SJ 195 0

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 14113 -
Reference Match 13868 98.26
5’ reference supported (transcript) 13998 99.19
3’ reference supported (transcript) 13952 98.86
5’ reference supported (gene) 14062 99.64
3’ reference supported (gene) 13977 99.04
Supported Reference Transcript Model (SRTM) 13943 98.8
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 627 -
5’ reference supported (transcript) 134 21.37
3’ reference supported (transcript) 115 18.34
5’ and 3’ reference supported (gene) 45 7.18
5’ reference supported (gene) 182 182
3’ reference supported (gene) 179 28.55
Supported Reference Transcript Model (SRTM) 45 7.18
Reference redundancy Level 1.06 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 231 -
5’ and 3’ reference supported (gene) 141 61.04
5’ reference supported (gene) 178 77.06
3’ reference supported (gene) 166 71.86
Intron retention incidence 40 17.32

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 213 -
5’ and 3’ reference supported (gene) 70 32.86
5’ reference supported (gene) 133 62.44
3’ reference supported (gene) 95 44.6
Non-canonical SJ incidence 7 3.29
Full Illumina SJ support 213 100
RT-switching incidence 22 10.33

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) 13237
Number of transcripts associated to TP (Reference Match) 13240
Partial True Positive detections (PTP) 725
Number of transcripts associated to PTP 760
False Negative (FN) 13314
False Positive (FP) 1190
Sensitivity 0.49
Precision 0.87
Non Redundant Precision 0.87
Positive Detection Rate 0.51
False Discovery Rate 0.13
False Detection Rate 0.08
Redundancy 1.01

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 20152
True Positive detections (TP) 12185
Number of transcripts associated to TP (Reference Match) 12186
Partial True Positive detections (PTP) 296
Number of transcripts associated to PTP 312
False Negative (FN) 7790
False Positive (FP) 2692
Sensitivity 0.6
Positive Detection Rate 0.61
Redundancy 1.01

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 15608
True Positive detections (TP) 10092
Number of transcripts associated to TP (Reference Match) 10093
Partial True Positive detections (PTP) 255
Number of transcripts associated to PTP 271
False Negative (FN) 5372
False Positive (FP) 4826
Sensitivity 0.65
Positive Detection Rate 0.66
Redundancy 1.01

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 9428
True Positive detections (TP) 6900
Number of transcripts associated to TP (Reference Match) 6901
Partial True Positive detections (PTP) 163
Number of transcripts associated to PTP 174
False Negative (FN) 2451
False Positive (FP) 8115
Sensitivity 0.73
Positive Detection Rate 0.74
Redundancy 1.01

Evaluation of novelty

Value
Number of isoforms simulated 7000
True Positive detections (TP) 1052
Number of transcripts associated to TP (Reference Match) 1054
Partial True Positive detections (PTP) 429
Number of transcripts associated to PTP 448
False Negative (FN) 5524
False Positive (FP) 13688
Sensitivity 0.15
Positive Detection Rate 0.21
Redundancy 1.02