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 605
Number of known genes detected 589
Number of transcripts detected 687
Number of transcripts associated to a known gene 662
Number of unique SJ detected 3838
Absolute value Relative value (%)
Novel SJ 214 0.06
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 407 -
Reference Match 209 51.35
5’ reference supported (transcript) 289 71.01
3’ reference supported (transcript) 294 72.24
5’ reference supported (gene) 371 91.15
3’ reference supported (gene) 344 84.52
5’ CAGE supported 6 1.47
3’ polyA supported 400 98.28
Supported Reference Transcript Model (SRTM) 362 88.94
Intra-priming 1 0.25
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 55 -
5’ reference supported (transcript) 6 10.91
3’ reference supported (transcript) 35 63.64
5’ and 3’ reference supported (gene) 12 21.82
5’ reference supported (gene) 15 15
3’ reference supported (gene) 46 83.64
5’ CAGE supported 0 0
3’ polyA supported 55 100
Supported Reference Transcript Model (SRTM) 15 27.27
Intra-priming 0 0
Reference redundancy Level 1 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 29 -
5’ and 3’ reference supported (gene) 20 68.97
5’ reference supported (gene) 20 68.97
3’ reference supported (gene) 28 96.55
5’ CAGE supported 0 0
3’ polyA supported 29 100
Supported Novel Transcript Model (SNTM) 19 65.52
Intra-priming 0 0
Intron retention incidence 9 31.03

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 171 -
5’ and 3’ reference supported (gene) 111 64.91
5’ reference supported (gene) 131 76.61
3’ reference supported (gene) 142 83.04
5’ CAGE supported 3 1.75
3’ polyA supported 164 95.91
Supported Novel Transcript Model (SNTM) 30 17.54
Non-canonical SJ incidence 0 0
Full Illumina SJ support 50 29.24
Intra-priming 1 0.58
RT-switching incidence 17 9.94

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) 33
SIRV transcripts associated to TP (Reference Match) 33
Partial True Positive detections (PTP) 2
SIRV transcripts associated to PTP 2
False Negative (FN) 49
False Positive (FP) 33
Sensitivity 0.39
Precision 0.49
Non Redundant Precision 0.49
Positive Detection Rate 0.42
False Discovery Rate 0.51
False Detection Rate 0.49
Redundancy 1