Your submission: ES_dRNA_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 12159
Number of known genes detected 11932
Number of transcripts detected 20637
Number of transcripts associated to a known gene 20365
Number of unique SJ detected 98824
Absolute value Relative value (%)
Novel SJ 1210 0.01
Non-canonical SJ 62 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 18615 -
Reference Match 18615 100
5’ reference supported (transcript) 18615 100
3’ reference supported (transcript) 18615 100
5’ reference supported (gene) 18615 100
3’ reference supported (gene) 18615 100
5’ CAGE supported 260 1.4
3’ polyA supported 14584 78.35
Supported Reference Transcript Model (SRTM) 18615 100
Intra-priming 916 4.92
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 789 -
5’ reference supported (transcript) 56 7.1
3’ reference supported (transcript) 554 70.22
5’ and 3’ reference supported (gene) 119 15.08
5’ reference supported (gene) 168 168
3’ reference supported (gene) 644 81.62
5’ CAGE supported 2 0.25
3’ polyA supported 754 95.56
Supported Reference Transcript Model (SRTM) 156 19.77
Intra-priming 2 0.25
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 304 -
5’ and 3’ reference supported (gene) 220 72.37
5’ reference supported (gene) 258 84.87
3’ reference supported (gene) 256 84.21
5’ CAGE supported 5 1.64
3’ polyA supported 293 96.38
Supported Novel Transcript Model (SNTM) 224 73.68
Intra-priming 0 0
Intron retention incidence 24 7.89

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 657 -
5’ and 3’ reference supported (gene) 354 53.88
5’ reference supported (gene) 457 69.56
3’ reference supported (gene) 486 73.97
5’ CAGE supported 12 1.83
3’ polyA supported 617 93.91
Supported Novel Transcript Model (SNTM) 82 12.48
Non-canonical SJ incidence 32 4.87
Full Illumina SJ support 201 30.59
Intra-priming 2 0.3
RT-switching incidence 74 11.26

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 68
True Positive detections (TP) 67
SIRV transcripts associated to TP (Reference Match) 67
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 17
False Positive (FP) 1
Sensitivity 0.8
Precision 0.99
Non Redundant Precision 0.99
Positive Detection Rate 0.8
False Discovery Rate 0.01
False Detection Rate 0.01
Redundancy 1