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 12114
Number of known genes detected 2835
Number of transcripts detected 14308
Number of transcripts associated to a known gene 4481
Number of unique SJ detected 16525
Absolute value Relative value (%)
Novel SJ 3797 0.23
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 1423 -
Reference Match 644 45.26
5’ reference supported (transcript) 988 69.43
3’ reference supported (transcript) 872 61.28
5’ reference supported (gene) 1153 81.03
3’ reference supported (gene) 1083 76.11
5’ CAGE supported 15 1.05
3’ polyA supported 1247 87.63
Supported Reference Transcript Model (SRTM) 1097 77.09
Intra-priming 6 0.42
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 363 -
5’ reference supported (transcript) 70 19.28
3’ reference supported (transcript) 171 47.11
5’ and 3’ reference supported (gene) 58 15.98
5’ reference supported (gene) 108 108
3’ reference supported (gene) 225 61.98
5’ CAGE supported 3 0.83
3’ polyA supported 277 76.31
Supported Reference Transcript Model (SRTM) 82 22.59
Intra-priming 2 0.55
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 728 -
5’ and 3’ reference supported (gene) 381 52.34
5’ reference supported (gene) 440 60.44
3’ reference supported (gene) 601 82.55
5’ CAGE supported 9 1.24
3’ polyA supported 696 95.6
Supported Novel Transcript Model (SNTM) 384 52.75
Intra-priming 0 0
Intron retention incidence 146 20.05

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 1967 -
5’ and 3’ reference supported (gene) 1296 65.89
5’ reference supported (gene) 1581 80.38
3’ reference supported (gene) 1565 79.56
5’ CAGE supported 34 1.73
3’ polyA supported 1860 94.56
Supported Novel Transcript Model (SNTM) 344 17.49
Non-canonical SJ incidence 0 0
Full Illumina SJ support 515 26.18
Intra-priming 2 0.1
RT-switching incidence 109 5.54

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 273
True Positive detections (TP) 21
SIRV transcripts associated to TP (Reference Match) 21
Partial True Positive detections (PTP) 1
SIRV transcripts associated to PTP 4
False Negative (FN) 62
False Positive (FP) 248
Sensitivity 0.25
Precision 0.08
Non Redundant Precision 0.08
Positive Detection Rate 0.26
False Discovery Rate 0.91
False Detection Rate 0.91
Redundancy 1.14