Your submission: WTC11_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 9187
Number of known genes detected 9139
Number of transcripts detected 33405
Number of transcripts associated to a known gene 32536
Number of unique SJ detected 86790
Absolute value Relative value (%)
Novel SJ 5800 0.07
Non-canonical SJ 10998 0.13

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 22692 -
Reference Match 14560 64.16
5’ reference supported (transcript) 20276 89.35
3’ reference supported (transcript) 15604 68.76
5’ reference supported (gene) 22136 97.55
3’ reference supported (gene) 19255 84.85
5’ CAGE supported 17947 79.09
3’ polyA supported 21170 93.29
Supported Reference Transcript Model (SRTM) 21730 95.76
Intra-priming 276 1.22
Reference redundancy Level 1.29 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1409 -
5’ reference supported (transcript) 624 44.29
3’ reference supported (transcript) 422 29.95
5’ and 3’ reference supported (gene) 382 27.11
5’ reference supported (gene) 925 925
3’ reference supported (gene) 751 53.3
5’ CAGE supported 925 65.65
3’ polyA supported 1129 80.13
Supported Reference Transcript Model (SRTM) 842 59.76
Intra-priming 15 1.06
Reference redundancy Level 1.15 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 3667 -
5’ and 3’ reference supported (gene) 2299 62.69
5’ reference supported (gene) 2737 74.64
3’ reference supported (gene) 2400 65.45
5’ CAGE supported 2454 66.92
3’ polyA supported 2761 75.29
Supported Novel Transcript Model (SNTM) 2439 66.51
Intra-priming 23 0.63
Intron retention incidence 462 12.6

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 4768 -
5’ and 3’ reference supported (gene) 2740 57.47
5’ reference supported (gene) 3611 75.73
3’ reference supported (gene) 3138 65.81
5’ CAGE supported 3520 73.83
3’ polyA supported 4003 83.96
Supported Novel Transcript Model (SNTM) 1239 25.99
Non-canonical SJ incidence 1778 37.29
Full Illumina SJ support 1347 28.25
Intra-priming 18 0.38
RT-switching incidence 257 5.39

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 103
True Positive detections (TP) 64
SIRV transcripts associated to TP (Reference Match) 64
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 2
False Negative (FN) 20
False Positive (FP) 37
Sensitivity 0.76
Precision 0.62
Non Redundant Precision 0.62
Positive Detection Rate 0.76
False Discovery Rate 0.36
False Detection Rate 0.36
Redundancy 1.03