Your submission: WTC11_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 387
Number of known genes detected 383
Number of transcripts detected 456
Number of transcripts associated to a known gene 449
Number of unique SJ detected 2070
Absolute value Relative value (%)
Novel SJ 137 0.07
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 286 -
Reference Match 156 54.55
5’ reference supported (transcript) 237 82.87
3’ reference supported (transcript) 193 67.48
5’ reference supported (gene) 274 95.8
3’ reference supported (gene) 260 90.91
5’ CAGE supported 248 86.71
3’ polyA supported 283 98.95
Supported Reference Transcript Model (SRTM) 277 96.85
Intra-priming 0 0
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 34 -
5’ reference supported (transcript) 1 2.94
3’ reference supported (transcript) 23 67.65
5’ and 3’ reference supported (gene) 10 29.41
5’ reference supported (gene) 12 12
3’ reference supported (gene) 31 91.18
5’ CAGE supported 3 8.82
3’ polyA supported 34 100
Supported Reference Transcript Model (SRTM) 14 41.18
Intra-priming 0 0
Reference redundancy Level 1.03 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 21 -
5’ and 3’ reference supported (gene) 16 76.19
5’ reference supported (gene) 19 90.48
3’ reference supported (gene) 18 85.71
5’ CAGE supported 18 85.71
3’ polyA supported 21 100
Supported Novel Transcript Model (SNTM) 19 90.48
Intra-priming 0 0
Intron retention incidence 2 9.52

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 108 -
5’ and 3’ reference supported (gene) 92 85.19
5’ reference supported (gene) 98 90.74
3’ reference supported (gene) 101 93.52
5’ CAGE supported 80 74.07
3’ polyA supported 108 100
Supported Novel Transcript Model (SNTM) 32 29.63
Non-canonical SJ incidence 0 0
Full Illumina SJ support 32 29.63
Intra-priming 0 0
RT-switching incidence 12 11.11

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 58
True Positive detections (TP) 32
SIRV transcripts associated to TP (Reference Match) 32
Partial True Positive detections (PTP) 2
SIRV transcripts associated to PTP 3
False Negative (FN) 50
False Positive (FP) 23
Sensitivity 0.38
Precision 0.55
Non Redundant Precision 0.55
Positive Detection Rate 0.4
False Discovery Rate 0.43
False Detection Rate 0.4
Redundancy 1.03