Your submission: WTC11_R2C2_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 3873
Number of known genes detected 3753
Number of transcripts detected 5587
Number of transcripts associated to a known gene 5414
Number of unique SJ detected 32711
Absolute value Relative value (%)
Novel SJ 1059 0.03
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 3385 -
Reference Match 1730 51.11
5’ reference supported (transcript) 2639 77.96
3’ reference supported (transcript) 2225 65.73
5’ reference supported (gene) 3124 92.29
3’ reference supported (gene) 2896 85.55
5’ CAGE supported 2896 85.55
3’ polyA supported 3306 97.67
Supported Reference Transcript Model (SRTM) 3229 95.39
Intra-priming 6 0.18
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 339 -
5’ reference supported (transcript) 218 64.31
3’ reference supported (transcript) 84 24.78
5’ and 3’ reference supported (gene) 115 33.92
5’ reference supported (gene) 269 269
3’ reference supported (gene) 164 48.38
5’ CAGE supported 265 78.17
3’ polyA supported 299 88.2
Supported Reference Transcript Model (SRTM) 255 75.22
Intra-priming 10 2.95
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 903 -
5’ and 3’ reference supported (gene) 750 83.06
5’ reference supported (gene) 859 95.13
3’ reference supported (gene) 786 87.04
5’ CAGE supported 791 87.6
3’ polyA supported 863 95.57
Supported Novel Transcript Model (SNTM) 771 85.38
Intra-priming 4 0.44
Intron retention incidence 278 30.79

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 787 -
5’ and 3’ reference supported (gene) 593 75.35
5’ reference supported (gene) 703 89.33
3’ reference supported (gene) 658 83.61
5’ CAGE supported 705 89.58
3’ polyA supported 768 97.59
Supported Novel Transcript Model (SNTM) 272 34.56
Non-canonical SJ incidence 0 0
Full Illumina SJ support 300 38.12
Intra-priming 5 0.64
RT-switching incidence 82 10.42

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 82
True Positive detections (TP) 45
SIRV transcripts associated to TP (Reference Match) 45
Partial True Positive detections (PTP) 8
SIRV transcripts associated to PTP 8
False Negative (FN) 31
False Positive (FP) 29
Sensitivity 0.54
Precision 0.55
Non Redundant Precision 0.55
Positive Detection Rate 0.63
False Discovery Rate 0.45
False Detection Rate 0.35
Redundancy 1