Your submission: WTC11_cdna_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 18870
Number of known genes detected 13021
Number of transcripts detected 45000
Number of transcripts associated to a known gene 38697
Number of unique SJ detected 87663
Absolute value Relative value (%)
Novel SJ 4062 0.05
Non-canonical SJ 307 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 26556 -
Reference Match 19798 74.55
5’ reference supported (transcript) 24091 90.72
3’ reference supported (transcript) 20599 77.57
5’ reference supported (gene) 25361 95.5
3’ reference supported (gene) 23800 89.62
5’ CAGE supported 18105 68.18
3’ polyA supported 23590 88.83
Supported Reference Transcript Model (SRTM) 25498 96.02
Intra-priming 536 2.02
Reference redundancy Level 1.1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2680 -
5’ reference supported (transcript) 365 13.62
3’ reference supported (transcript) 1278 47.69
5’ and 3’ reference supported (gene) 270 10.07
5’ reference supported (gene) 588 588
3’ reference supported (gene) 1644 61.34
5’ CAGE supported 655 24.44
3’ polyA supported 2491 92.95
Supported Reference Transcript Model (SRTM) 700 26.12
Intra-priming 26 0.97
Reference redundancy Level 1.11 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 9331 -
5’ and 3’ reference supported (gene) 7342 78.68
5’ reference supported (gene) 8612 92.29
3’ reference supported (gene) 7817 83.77
5’ CAGE supported 8142 87.26
3’ polyA supported 9191 98.5
Supported Novel Transcript Model (SNTM) 6809 72.97
Intra-priming 46 0.49
Intron retention incidence 1169 12.53

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 130 -
5’ and 3’ reference supported (gene) 64 49.23
5’ reference supported (gene) 86 66.15
3’ reference supported (gene) 100 76.92
5’ CAGE supported 84 64.62
3’ polyA supported 122 93.85
Supported Novel Transcript Model (SNTM) 2 1.54
Non-canonical SJ incidence 122 93.85
Full Illumina SJ support 2 1.54
Intra-priming 3 2.31
RT-switching incidence 67 51.54

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 105
True Positive detections (TP) 76
SIRV transcripts associated to TP (Reference Match) 76
Partial True Positive detections (PTP) 4
SIRV transcripts associated to PTP 5
False Negative (FN) 4
False Positive (FP) 24
Sensitivity 0.9
Precision 0.72
Non Redundant Precision 0.72
Positive Detection Rate 0.95
False Discovery Rate 0.27
False Detection Rate 0.23
Redundancy 1.01