Your submission: WTC11_CapTrap_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 15651
Number of known genes detected 15356
Number of transcripts detected 39544
Number of transcripts associated to a known gene 39208
Number of unique SJ detected 95798
Absolute value Relative value (%)
Novel SJ 851 0.01
Non-canonical SJ 53 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 38078 -
Reference Match 37565 98.65
5’ reference supported (transcript) 37774 99.2
3’ reference supported (transcript) 37770 99.19
5’ reference supported (gene) 37934 99.62
3’ reference supported (gene) 37869 99.45
5’ CAGE supported 23577 61.92
3’ polyA supported 28942 76.01
Supported Reference Transcript Model (SRTM) 37851 99.4
Intra-priming 1133 2.98
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 631 -
5’ reference supported (transcript) 167 26.47
3’ reference supported (transcript) 261 41.36
5’ and 3’ reference supported (gene) 97 15.37
5’ reference supported (gene) 267 267
3’ reference supported (gene) 379 60.06
5’ CAGE supported 353 55.94
3’ polyA supported 556 88.11
Supported Reference Transcript Model (SRTM) 348 55.15
Intra-priming 23 3.65
Reference redundancy Level 1.01 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 167 -
5’ and 3’ reference supported (gene) 108 64.67
5’ reference supported (gene) 147 88.02
3’ reference supported (gene) 123 73.65
5’ CAGE supported 146 87.43
3’ polyA supported 166 99.4
Supported Novel Transcript Model (SNTM) 140 83.83
Intra-priming 1 0.6
Intron retention incidence 16 9.58

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 332 -
5’ and 3’ reference supported (gene) 131 39.46
5’ reference supported (gene) 237 71.39
3’ reference supported (gene) 175 52.71
5’ CAGE supported 279 84.04
3’ polyA supported 319 96.08
Supported Novel Transcript Model (SNTM) 152 45.78
Non-canonical SJ incidence 17 5.12
Full Illumina SJ support 181 54.52
Intra-priming 3 0.9
RT-switching incidence 20 6.02

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 73
True Positive detections (TP) 69
SIRV transcripts associated to TP (Reference Match) 69
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 1
False Negative (FN) 15
False Positive (FP) 3
Sensitivity 0.82
Precision 0.95
Non Redundant Precision 0.95
Positive Detection Rate 0.82
False Discovery Rate 0.04
False Detection Rate 0.04
Redundancy 1.01