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 10577
Number of known genes detected 10527
Number of transcripts detected 19181
Number of transcripts associated to a known gene 19075
Number of unique SJ detected 55454
Absolute value Relative value (%)
Novel SJ 560 0.01
Non-canonical SJ 146 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 7559 -
Reference Match 4932 65.25
5’ reference supported (transcript) 6633 87.75
3’ reference supported (transcript) 5027 66.5
5’ reference supported (gene) 6996 92.55
3’ reference supported (gene) 5184 68.58
Supported Reference Transcript Model (SRTM) 5093 67.38
Reference redundancy Level 1.05 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 10267 -
5’ reference supported (transcript) 1284 12.51
3’ reference supported (transcript) 1179 11.48
5’ and 3’ reference supported (gene) 64 0.62
5’ reference supported (gene) 1722 1722
3’ reference supported (gene) 1589 15.48
Supported Reference Transcript Model (SRTM) 64 0.62
Reference redundancy Level 1.34 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 821 -
5’ and 3’ reference supported (gene) 64 7.8
5’ reference supported (gene) 155 18.88
3’ reference supported (gene) 224 27.28
Intron retention incidence 27 3.29

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 428 -
5’ and 3’ reference supported (gene) 76 17.76
5’ reference supported (gene) 161 37.62
3’ reference supported (gene) 150 35.05
Non-canonical SJ incidence 10 2.34
Full Illumina SJ support 428 100
RT-switching incidence 14 3.27

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) 3964
Number of transcripts associated to TP (Reference Match) 3979
Partial True Positive detections (PTP) 8671
Number of transcripts associated to PTP 11499
False Negative (FN) 14938
False Positive (FP) 3703
Sensitivity 0.15
Precision 0.21
Non Redundant Precision 0.21
Positive Detection Rate 0.45
False Discovery Rate 0.65
False Detection Rate 0.19
Redundancy 1.27

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 20152
True Positive detections (TP) 3807
Number of transcripts associated to TP (Reference Match) 3822
Partial True Positive detections (PTP) 6829
Number of transcripts associated to PTP 9107
False Negative (FN) 9926
False Positive (FP) 6252
Sensitivity 0.19
Positive Detection Rate 0.51
Redundancy 1.26

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) 3125
Partial True Positive detections (PTP) 6368
Number of transcripts associated to PTP 8574
False Negative (FN) 6492
False Positive (FP) 7482
Sensitivity 0.2
Positive Detection Rate 0.58
Redundancy 1.28

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) 2137
Partial True Positive detections (PTP) 4909
Number of transcripts associated to PTP 6889
False Negative (FN) 2670
False Positive (FP) 10155
Sensitivity 0.23
Positive Detection Rate 0.72
Redundancy 1.34

Evaluation of novelty

Value
Number of isoforms simulated 7000
True Positive detections (TP) 157
Number of transcripts associated to TP (Reference Match) 157
Partial True Positive detections (PTP) 1842
Number of transcripts associated to PTP 2392
False Negative (FN) 5012
False Positive (FP) 16632
Sensitivity 0.02
Positive Detection Rate 0.28
Redundancy 1.28