Your submission: ES_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 12824
Number of known genes detected 9739
Number of transcripts detected 21287
Number of transcripts associated to a known gene 17506
Number of unique SJ detected 77941
Absolute value Relative value (%)
Novel SJ 9024 0.12
Non-canonical SJ 2480 0.03

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 8820 -
Reference Match 3436 38.96
5’ reference supported (transcript) 5773 65.45
3’ reference supported (transcript) 5193 58.88
5’ reference supported (gene) 7492 84.94
3’ reference supported (gene) 6698 75.94
5’ CAGE supported 174 1.97
3’ polyA motif supported 174 1.97
Supported Reference Transcript Model (SRTM) 5735 65.02
Reference redundancy Level 1.03 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 3783 -
5’ reference supported (transcript) 585 15.46
3’ reference supported (transcript) 1775 46.92
5’ and 3’ reference supported (gene) 289 7.64
5’ reference supported (gene) 930 930
3’ reference supported (gene) 2319 61.3
5’ CAGE supported 28 0.74
3’ polyA motif supported 28 0.74
Supported Reference Transcript Model (SRTM) 292 7.72
Reference redundancy Level 1.21 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1115 -
5’ and 3’ reference supported (gene) 679 60.9
5’ reference supported (gene) 954 85.56
3’ reference supported (gene) 787 70.58
5’ CAGE supported 20 1.79
3’ polyA motif supported 20 1.79
Supported Novel Transcript Model (SNTM) 616 55.25
Intron retention incidence 196 17.58

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 3788 -
5’ and 3’ reference supported (gene) 1789 47.23
5’ reference supported (gene) 2612 68.95
3’ reference supported (gene) 2467 65.13
5’ CAGE supported 54 1.43
3’ polyA motif supported 54 1.43
Supported Novel Transcript Model (SNTM) 272 7.18
Non-canonical SJ incidence 1672 44.14
Full Illumina SJ support 950 25.08
RT-switching incidence 293 7.73

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 24
True Positive detections (TP) 16
SIRV transcripts associated to TP (Reference Match) 16
Partial True Positive detections (PTP) 1
SIRV transcripts associated to PTP 2
False Negative (FN) 67
False Positive (FP) 6
Sensitivity 0.19
Precision 0.67
Non Redundant Precision 0.67
Positive Detection Rate 0.2
False Discovery Rate 0.29
False Detection Rate 0.25
Redundancy 1.06