Your submission: ES_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 4223
Number of known genes detected 3793
Number of transcripts detected 5659
Number of transcripts associated to a known gene 5154
Number of unique SJ detected 34509
Absolute value Relative value (%)
Novel SJ 1253 0.04
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 3155 -
Reference Match 1615 51.19
5’ reference supported (transcript) 2303 73
3’ reference supported (transcript) 2150 68.15
5’ reference supported (gene) 2736 86.72
3’ reference supported (gene) 2559 81.11
5’ CAGE supported 62 1.97
3’ polyA supported 2884 91.41
Supported Reference Transcript Model (SRTM) 2600 82.41
Intra-priming 8 0.25
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 281 -
5’ reference supported (transcript) 115 40.93
3’ reference supported (transcript) 111 39.5
5’ and 3’ reference supported (gene) 74 26.33
5’ reference supported (gene) 161 161
3’ reference supported (gene) 157 55.87
5’ CAGE supported 6 2.14
3’ polyA supported 212 75.44
Supported Reference Transcript Model (SRTM) 125 44.48
Intra-priming 5 1.78
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 710 -
5’ and 3’ reference supported (gene) 561 79.01
5’ reference supported (gene) 661 93.1
3’ reference supported (gene) 599 84.37
5’ CAGE supported 14 1.97
3’ polyA supported 653 91.97
Supported Novel Transcript Model (SNTM) 579 81.55
Intra-priming 7 0.99
Intron retention incidence 188 26.48

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 1008 -
5’ and 3’ reference supported (gene) 668 66.27
5’ reference supported (gene) 814 80.75
3’ reference supported (gene) 822 81.55
5’ CAGE supported 22 2.18
3’ polyA supported 960 95.24
Supported Novel Transcript Model (SNTM) 307 30.46
Non-canonical SJ incidence 0 0
Full Illumina SJ support 448 44.44
Intra-priming 2 0.2
RT-switching incidence 97 9.62

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 84
True Positive detections (TP) 46
SIRV transcripts associated to TP (Reference Match) 46
Partial True Positive detections (PTP) 8
SIRV transcripts associated to PTP 9
False Negative (FN) 30
False Positive (FP) 29
Sensitivity 0.55
Precision 0.55
Non Redundant Precision 0.55
Positive Detection Rate 0.64
False Discovery Rate 0.44
False Detection Rate 0.35
Redundancy 1.02