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 12117
Number of known genes detected 11698
Number of transcripts detected 27028
Number of transcripts associated to a known gene 26365
Number of unique SJ detected 116552
Absolute value Relative value (%)
Novel SJ 5649 0.05
Non-canonical SJ 134 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 13197 -
Reference Match 5526 41.87
5’ reference supported (transcript) 9194 69.67
3’ reference supported (transcript) 7881 59.72
5’ reference supported (gene) 11508 87.2
3’ reference supported (gene) 10205 77.33
5’ CAGE supported 289 2.19
3’ polyA motif supported 289 2.19
Supported Reference Transcript Model (SRTM) 8973 67.99
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 4836 -
5’ reference supported (transcript) 1974 40.82
3’ reference supported (transcript) 1418 29.32
5’ and 3’ reference supported (gene) 741 15.32
5’ reference supported (gene) 2712 2712
3’ reference supported (gene) 2160 44.67
5’ CAGE supported 88 1.82
3’ polyA motif supported 88 1.82
Supported Reference Transcript Model (SRTM) 747 15.45
Reference redundancy Level 1.28 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 4292 -
5’ and 3’ reference supported (gene) 2890 67.33
5’ reference supported (gene) 3656 85.18
3’ reference supported (gene) 3369 78.49
5’ CAGE supported 63 1.47
3’ polyA motif supported 63 1.47
Supported Novel Transcript Model (SNTM) 2691 62.7
Intron retention incidence 1258 29.31

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 4040 -
5’ and 3’ reference supported (gene) 1867 46.21
5’ reference supported (gene) 2727 67.5
3’ reference supported (gene) 2756 68.22
5’ CAGE supported 80 1.98
3’ polyA motif supported 80 1.98
Supported Novel Transcript Model (SNTM) 886 21.93
Non-canonical SJ incidence 161 3.99
Full Illumina SJ support 2145 53.09
RT-switching incidence 373 9.23

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 28
True Positive detections (TP) 22
SIRV transcripts associated to TP (Reference Match) 22
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 62
False Positive (FP) 6
Sensitivity 0.26
Precision 0.79
Non Redundant Precision 0.79
Positive Detection Rate 0.26
False Discovery Rate 0.21
False Detection Rate 0.21
Redundancy 1