Your submission: WTC11_CapTrap_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 4657
Number of known genes detected 4290
Number of transcripts detected 8466
Number of transcripts associated to a known gene 7689
Number of unique SJ detected 19178
Absolute value Relative value (%)
Novel SJ 3675 0.19
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 2056 -
Reference Match 937 45.57
5’ reference supported (transcript) 1508 73.35
3’ reference supported (transcript) 1280 62.26
5’ reference supported (gene) 1768 85.99
3’ reference supported (gene) 1703 82.83
5’ CAGE supported 1569 76.31
3’ polyA supported 2021 98.3
Supported Reference Transcript Model (SRTM) 1822 88.62
Intra-priming 4 0.19
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1493 -
5’ reference supported (transcript) 166 11.12
3’ reference supported (transcript) 826 55.32
5’ and 3’ reference supported (gene) 132 8.84
5’ reference supported (gene) 257 257
3’ reference supported (gene) 1122 75.15
5’ CAGE supported 294 19.69
3’ polyA supported 1467 98.26
Supported Reference Transcript Model (SRTM) 331 22.17
Intra-priming 1 0.07
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1366 -
5’ and 3’ reference supported (gene) 823 60.25
5’ reference supported (gene) 903 66.11
3’ reference supported (gene) 1211 88.65
5’ CAGE supported 861 63.03
3’ polyA supported 1362 99.71
Supported Novel Transcript Model (SNTM) 784 57.39
Intra-priming 1 0.07
Intron retention incidence 151 11.05

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 2774 -
5’ and 3’ reference supported (gene) 2179 78.55
5’ reference supported (gene) 2484 89.55
3’ reference supported (gene) 2389 86.12
5’ CAGE supported 2486 89.62
3’ polyA supported 2748 99.06
Supported Novel Transcript Model (SNTM) 798 28.77
Non-canonical SJ incidence 0 0
Full Illumina SJ support 871 31.4
Intra-priming 3 0.11
RT-switching incidence 124 4.47

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 287
True Positive detections (TP) 26
SIRV transcripts associated to TP (Reference Match) 26
Partial True Positive detections (PTP) 6
SIRV transcripts associated to PTP 9
False Negative (FN) 52
False Positive (FP) 252
Sensitivity 0.31
Precision 0.09
Non Redundant Precision 0.09
Positive Detection Rate 0.38
False Discovery Rate 0.9
False Detection Rate 0.88
Redundancy 1.09