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 6045
Number of known genes detected 6045
Number of transcripts detected 11607
Number of transcripts associated to a known gene 11605
Number of unique SJ detected 54119
Absolute value Relative value (%)
Novel SJ 560 0.01
Non-canonical SJ 190 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 10453 -
Reference Match 6793 64.99
5’ reference supported (transcript) 9396 89.89
3’ reference supported (transcript) 7305 69.88
5’ reference supported (gene) 10255 98.11
3’ reference supported (gene) 9233 88.33
5’ CAGE supported 8671 82.95
3’ polyA supported 10318 98.71
Supported Reference Transcript Model (SRTM) 10288 98.42
Intra-priming 61 0.58
Reference redundancy Level 1.18 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 294 -
5’ reference supported (transcript) 30 10.2
3’ reference supported (transcript) 169 57.48
5’ and 3’ reference supported (gene) 90 30.61
5’ reference supported (gene) 114 114
3’ reference supported (gene) 245 83.33
5’ CAGE supported 106 36.05
3’ polyA supported 287 97.62
Supported Reference Transcript Model (SRTM) 149 50.68
Intra-priming 1 0.34
Reference redundancy Level 1.11 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 342 -
5’ and 3’ reference supported (gene) 303 88.6
5’ reference supported (gene) 327 95.61
3’ reference supported (gene) 315 92.11
5’ CAGE supported 283 82.75
3’ polyA supported 342 100
Supported Novel Transcript Model (SNTM) 298 87.13
Intra-priming 2 0.58
Intron retention incidence 39 11.4

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 516 -
5’ and 3’ reference supported (gene) 389 75.39
5’ reference supported (gene) 452 87.6
3’ reference supported (gene) 443 85.85
5’ CAGE supported 437 84.69
3’ polyA supported 514 99.61
Supported Novel Transcript Model (SNTM) 121 23.45
Non-canonical SJ incidence 142 27.52
Full Illumina SJ support 128 24.81
Intra-priming 0 0
RT-switching incidence 47 9.11

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 71
True Positive detections (TP) 66
SIRV transcripts associated to TP (Reference Match) 66
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 18
False Positive (FP) 5
Sensitivity 0.79
Precision 0.93
Non Redundant Precision 0.93
Positive Detection Rate 0.79
False Discovery Rate 0.07
False Detection Rate 0.07
Redundancy 1