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 37649
Number of known genes detected 12293
Number of transcripts detected 54036
Number of transcripts associated to a known gene 28259
Number of unique SJ detected 83829
Absolute value Relative value (%)
Novel SJ 2463 0.03
Non-canonical SJ 208 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 20831 -
Reference Match 15887 76.27
5’ reference supported (transcript) 18373 88.2
3’ reference supported (transcript) 16475 79.09
5’ reference supported (gene) 19550 93.85
3’ reference supported (gene) 18181 87.28
5’ CAGE supported 328 1.57
3’ polyA supported 16782 80.56
Supported Reference Transcript Model (SRTM) 19218 92.26
Intra-priming 640 3.07
Reference redundancy Level 1.12 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1422 -
5’ reference supported (transcript) 157 11.04
3’ reference supported (transcript) 712 50.07
5’ and 3’ reference supported (gene) 119 8.37
5’ reference supported (gene) 278 278
3’ reference supported (gene) 844 59.35
5’ CAGE supported 8 0.56
3’ polyA supported 1139 80.1
Supported Reference Transcript Model (SRTM) 228 16.03
Intra-priming 39 2.74
Reference redundancy Level 1.08 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 6005 -
5’ and 3’ reference supported (gene) 4367 72.72
5’ reference supported (gene) 5359 89.24
3’ reference supported (gene) 4832 80.47
5’ CAGE supported 101 1.68
3’ polyA supported 5710 95.09
Supported Novel Transcript Model (SNTM) 4201 69.96
Intra-priming 48 0.8
Intron retention incidence 1011 16.84

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 1 -
5’ and 3’ reference supported (gene) 1 100
5’ reference supported (gene) 1 100
3’ reference supported (gene) 1 100
5’ CAGE supported 0 0
3’ polyA supported 1 100
Supported Novel Transcript Model (SNTM) 0 0
Non-canonical SJ incidence 1 100
Full Illumina SJ support 0 0
Intra-priming 0 0
RT-switching incidence 0 0

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 100
True Positive detections (TP) 75
SIRV transcripts associated to TP (Reference Match) 75
Partial True Positive detections (PTP) 5
SIRV transcripts associated to PTP 7
False Negative (FN) 4
False Positive (FP) 18
Sensitivity 0.89
Precision 0.75
Non Redundant Precision 0.75
Positive Detection Rate 0.95
False Discovery Rate 0.23
False Detection Rate 0.18
Redundancy 1.02