Your submission: ES_CapTrap_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 12964
Number of known genes detected 10808
Number of transcripts detected 23485
Number of transcripts associated to a known gene 20672
Number of unique SJ detected 73790
Absolute value Relative value (%)
Novel SJ 7648 0.1
Non-canonical SJ 137 0.0

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 9416 -
Reference Match 3526 37.45
5’ reference supported (transcript) 6262 66.5
3’ reference supported (transcript) 5252 55.78
5’ reference supported (gene) 7963 84.57
3’ reference supported (gene) 6949 73.8
5’ CAGE supported 226 2.4
3’ polyA motif supported 226 2.4
Supported Reference Transcript Model (SRTM) 5914 62.81
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 6489 -
5’ reference supported (transcript) 1541 23.75
3’ reference supported (transcript) 2554 39.36
5’ and 3’ reference supported (gene) 563 8.68
5’ reference supported (gene) 2235 2235
3’ reference supported (gene) 3480 53.63
5’ CAGE supported 78 1.2
3’ polyA motif supported 78 1.2
Supported Reference Transcript Model (SRTM) 571 8.8
Reference redundancy Level 1.22 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1505 -
5’ and 3’ reference supported (gene) 928 61.66
5’ reference supported (gene) 1278 84.92
3’ reference supported (gene) 1095 72.76
5’ CAGE supported 34 2.26
3’ polyA motif supported 34 2.26
Supported Novel Transcript Model (SNTM) 824 54.75
Intron retention incidence 185 12.29

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 3262 -
5’ and 3’ reference supported (gene) 896 27.47
5’ reference supported (gene) 1764 54.08
3’ reference supported (gene) 1696 51.99
5’ CAGE supported 52 1.59
3’ polyA motif supported 52 1.59
Supported Novel Transcript Model (SNTM) 328 10.06
Non-canonical SJ incidence 98 3
Full Illumina SJ support 1525 46.75
RT-switching incidence 202 6.19

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 54
True Positive detections (TP) 31
SIRV transcripts associated to TP (Reference Match) 31
Partial True Positive detections (PTP) 3
SIRV transcripts associated to PTP 4
False Negative (FN) 50
False Positive (FP) 19
Sensitivity 0.37
Precision 0.57
Non Redundant Precision 0.57
Positive Detection Rate 0.4
False Discovery Rate 0.41
False Detection Rate 0.35
Redundancy 1.03