Your submission: mouse_simulation_cDNA_PacBio 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 13874
Number of known genes detected 13839
Number of transcripts detected 34728
Number of transcripts associated to a known gene 34595
Number of unique SJ detected 151103
Absolute value Relative value (%)
Novel SJ 7240 0.05
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 25039 -
Reference Match 24686 98.59
5’ reference supported (transcript) 24903 99.46
3’ reference supported (transcript) 24756 98.87
5’ reference supported (gene) 24994 99.82
3’ reference supported (gene) 24965 99.7
Supported Reference Transcript Model (SRTM) 24941 99.61
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 205 -
5’ reference supported (transcript) 28 13.66
3’ reference supported (transcript) 117 57.07
5’ and 3’ reference supported (gene) 65 31.71
5’ reference supported (gene) 83 83
3’ reference supported (gene) 185 90.24
Supported Reference Transcript Model (SRTM) 65 31.71
Reference redundancy Level 1.01 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 953 -
5’ and 3’ reference supported (gene) 760 79.75
5’ reference supported (gene) 772 81.01
3’ reference supported (gene) 939 98.53
Intron retention incidence 60 6.3

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 8398 -
5’ and 3’ reference supported (gene) 8093 96.37
5’ reference supported (gene) 8173 97.32
3’ reference supported (gene) 8290 98.71
Non-canonical SJ incidence 0 0
Full Illumina SJ support 8398 100
RT-switching incidence 419 4.99

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) 24634
Number of transcripts associated to TP (Reference Match) 24634
Partial True Positive detections (PTP) 383
Number of transcripts associated to PTP 384
False Negative (FN) 2169
False Positive (FP) 9710
Sensitivity 0.91
Precision 0.71
Non Redundant Precision 0.71
Positive Detection Rate 0.92
False Discovery Rate 0.29
False Detection Rate 0.28
Redundancy 1

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 20152
True Positive detections (TP) 18518
Number of transcripts associated to TP (Reference Match) 18518
Partial True Positive detections (PTP) 282
Number of transcripts associated to PTP 283
False Negative (FN) 1376
False Positive (FP) 15927
Sensitivity 0.92
Positive Detection Rate 0.93
Redundancy 1

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 15608
True Positive detections (TP) 14476
Number of transcripts associated to TP (Reference Match) 14476
Partial True Positive detections (PTP) 200
Number of transcripts associated to PTP 201
False Negative (FN) 948
False Positive (FP) 20051
Sensitivity 0.93
Positive Detection Rate 0.94
Redundancy 1

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 9428
True Positive detections (TP) 8900
Number of transcripts associated to TP (Reference Match) 8900
Partial True Positive detections (PTP) 96
Number of transcripts associated to PTP 97
False Negative (FN) 445
False Positive (FP) 25731
Sensitivity 0.94
Positive Detection Rate 0.95
Redundancy 1

Evaluation of novelty

Value
Number of isoforms simulated 7000
True Positive detections (TP) 6116
Number of transcripts associated to TP (Reference Match) 6116
Partial True Positive detections (PTP) 101
Number of transcripts associated to PTP 101
False Negative (FN) 793
False Positive (FP) 28511
Sensitivity 0.87
Positive Detection Rate 0.89
Redundancy 1