Your submission: WTC11_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. SIRV 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 1. and 3. 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

Here, SIRVs are not taken into account for none of the metrics.

Global overview

Value
Number of genes detected 12382
Number of known genes detected 12361
Number of transcripts detected 22572
Number of transcripts associated to a known gene 22523
Number of unique SJ detected 123020
Absolute value Relative value (%)
Novel SJ 504 0
Non-canonical SJ 143 0

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 21405 -
Reference Match 21123 98.68
5’ reference supported (transcript) 21215 99.11
3’ reference supported (transcript) 21255 99.3
5’ reference supported (gene) 21312 99.57
3’ reference supported (gene) 21306 99.54
5’ CAGE supported 16691 77.98
3’ polyA supported 19384 90.56
Supported Reference Transcript Model (SRTM) 21292 99.47
Intra-priming 331 1.55
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 139 -
5’ reference supported (transcript) 43 30.94
3’ reference supported (transcript) 50 35.97
5’ and 3’ reference supported (gene) 49 35.25
5’ reference supported (gene) 84 84
3’ reference supported (gene) 92 66.19
5’ CAGE supported 84 60.43
3’ polyA supported 135 97.12
Supported Reference Transcript Model (SRTM) 102 73.38
Intra-priming 0 0
Reference redundancy Level 1.01 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 717 -
5’ and 3’ reference supported (gene) 526 73.36
5’ reference supported (gene) 604 84.24
3’ reference supported (gene) 619 86.33
5’ CAGE supported 539 75.17
3’ polyA supported 714 99.58
Supported Novel Transcript Model (SNTM) 576 80.33
Intra-priming 3 0.42
Intron retention incidence 115 16.04

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 262 -
5’ and 3’ reference supported (gene) 106 40.46
5’ reference supported (gene) 146 55.73
3’ reference supported (gene) 177 67.56
5’ CAGE supported 177 67.56
3’ polyA supported 258 98.47
Supported Novel Transcript Model (SNTM) 155 59.16
Non-canonical SJ incidence 43 16.41
Full Illumina SJ support 205 78.24
Intra-priming 3 1.15
RT-switching incidence 28 10.69

Evaluation of Spike-Ins (SIRVs)

The following metrics and definitions apply to SIRV transcripts:

ATENTION If in this chunk of the evaluation all the results are 0, please, check if the reference genome and/or transcriptome used for building your transcript-model contain information about spike-ins.

Value
SIRV transcripts 77
True Positive detections (TP) 75
SIRV transcripts associated to TP (Reference Match) 75
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 9
False Positive (FP) 2
Sensitivity 0.89
Precision 0.97
Non Redundant Precision 0.97
Positive Detection Rate 0.89
False Discovery Rate 0.03
False Detection Rate 0.03
Redundancy 1