Your submission: mouse_sim_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 14028
Number of known genes detected 14028
Number of transcripts detected 24020
Number of transcripts associated to a known gene 23996
Number of unique SJ detected 144942
Absolute value Relative value (%)
Novel SJ 198 0
Non-canonical SJ 371 0

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 23497 -
Reference Match 23345 99.35
5’ reference supported (transcript) 23435 99.74
3’ reference supported (transcript) 23374 99.48
5’ reference supported (gene) 23460 99.84
3’ reference supported (gene) 23397 99.57
Supported Reference Transcript Model (SRTM) 23379 99.5
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 79 -
5’ reference supported (transcript) 26 32.91
3’ reference supported (transcript) 14 17.72
5’ and 3’ reference supported (gene) 52 65.82
5’ reference supported (gene) 63 63
3’ reference supported (gene) 65 82.28
Supported Reference Transcript Model (SRTM) 52 65.82
Reference redundancy Level 1.03 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 304 -
5’ and 3’ reference supported (gene) 263 86.51
5’ reference supported (gene) 284 93.42
3’ reference supported (gene) 278 91.45
Intron retention incidence 25 8.22

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 116 -
5’ and 3’ reference supported (gene) 67 57.76
5’ reference supported (gene) 98 84.48
3’ reference supported (gene) 79 68.1
Non-canonical SJ incidence 46 39.66
Full Illumina SJ support 116 100
RT-switching incidence 34 29.31

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) 22855
Number of transcripts associated to TP (Reference Match) 22867
Partial True Positive detections (PTP) 190
Number of transcripts associated to PTP 190
False Negative (FN) 4136
False Positive (FP) 963
Sensitivity 0.84
Precision 0.95
Non Redundant Precision 0.95
Positive Detection Rate 0.85
False Discovery Rate 0.05
False Detection Rate 0.04
Redundancy 1

Evaluation of all GENCODE simulation

Value
Number of isoforms simulated 20152
True Positive detections (TP) 19162
Number of transcripts associated to TP (Reference Match) 19164
Partial True Positive detections (PTP) 70
Number of transcripts associated to PTP 70
False Negative (FN) 936
False Positive (FP) 4786
Sensitivity 0.95
Positive Detection Rate 0.95
Redundancy 1

Evaluation of only GENCODE transcripts simulated

Value
Number of isoforms simulated 15608
True Positive detections (TP) 14810
Number of transcripts associated to TP (Reference Match) 14812
Partial True Positive detections (PTP) 59
Number of transcripts associated to PTP 59
False Negative (FN) 752
False Positive (FP) 9149
Sensitivity 0.95
Positive Detection Rate 0.95
Redundancy 1

Evaluation of only GENCODE transcripts simulated with TPM >= 5

Value
Number of isoforms simulated 9428
True Positive detections (TP) 8932
Number of transcripts associated to TP (Reference Match) 8934
Partial True Positive detections (PTP) 28
Number of transcripts associated to PTP 28
False Negative (FN) 474
False Positive (FP) 15058
Sensitivity 0.95
Positive Detection Rate 0.95
Redundancy 1

Evaluation of novelty

Value
Number of isoforms simulated 7000
True Positive detections (TP) 3693
Number of transcripts associated to TP (Reference Match) 3703
Partial True Positive detections (PTP) 120
Number of transcripts associated to PTP 120
False Negative (FN) 3200
False Positive (FP) 20197
Sensitivity 0.53
Positive Detection Rate 0.54
Redundancy 1.01