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 14060
Number of known genes detected 13798
Number of transcripts detected 29702
Number of transcripts associated to a known gene 29376
Number of unique SJ detected 120943
Absolute value Relative value (%)
Novel SJ 841 0.01
Non-canonical SJ 68 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 27009 -
Reference Match 26670 98.74
5’ reference supported (transcript) 26783 99.16
3’ reference supported (transcript) 26822 99.31
5’ reference supported (gene) 26893 99.57
3’ reference supported (gene) 26876 99.51
5’ CAGE supported 17826 66
3’ polyA supported 23232 86.02
Supported Reference Transcript Model (SRTM) 26860 99.45
Intra-priming 516 1.91
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1474 -
5’ reference supported (transcript) 125 8.48
3’ reference supported (transcript) 945 64.11
5’ and 3’ reference supported (gene) 273 18.52
5’ reference supported (gene) 376 376
3’ reference supported (gene) 1222 82.9
5’ CAGE supported 331 22.46
3’ polyA supported 1431 97.08
Supported Reference Transcript Model (SRTM) 480 32.56
Intra-priming 5 0.34
Reference redundancy Level 1.05 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 651 -
5’ and 3’ reference supported (gene) 490 75.27
5’ reference supported (gene) 553 84.95
3’ reference supported (gene) 573 88.02
5’ CAGE supported 550 84.49
3’ polyA supported 644 98.92
Supported Novel Transcript Model (SNTM) 511 78.49
Intra-priming 4 0.61
Intron retention incidence 126 19.35

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 242 -
5’ and 3’ reference supported (gene) 77 31.82
5’ reference supported (gene) 136 56.2
3’ reference supported (gene) 133 54.96
5’ CAGE supported 185 76.45
3’ polyA supported 240 99.17
Supported Novel Transcript Model (SNTM) 171 70.66
Non-canonical SJ incidence 12 4.96
Full Illumina SJ support 199 82.23
Intra-priming 2 0.83
RT-switching incidence 20 8.26

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 79
True Positive detections (TP) 78
SIRV transcripts associated to TP (Reference Match) 78
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 6
False Positive (FP) 1
Sensitivity 0.93
Precision 0.99
Non Redundant Precision 0.99
Positive Detection Rate 0.93
False Discovery Rate 0.01
False Detection Rate 0.01
Redundancy 1