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 15020
Number of known genes detected 14796
Number of transcripts detected 39519
Number of transcripts associated to a known gene 38861
Number of unique SJ detected 130318
Absolute value Relative value (%)
Novel SJ 4416 0.03
Non-canonical SJ 751 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 32657 -
Reference Match 32114 98.34
5’ reference supported (transcript) 32320 98.97
3’ reference supported (transcript) 32361 99.09
5’ reference supported (gene) 32507 99.54
3’ reference supported (gene) 32482 99.46
5’ CAGE supported 22882 70.07
3’ polyA supported 27167 83.19
Supported Reference Transcript Model (SRTM) 32446 99.35
Intra-priming 795 2.43
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1008 -
5’ reference supported (transcript) 381 37.8
3’ reference supported (transcript) 214 21.23
5’ and 3’ reference supported (gene) 249 24.7
5’ reference supported (gene) 623 623
3’ reference supported (gene) 474 47.02
5’ CAGE supported 565 56.05
3’ polyA supported 935 92.76
Supported Reference Transcript Model (SRTM) 696 69.05
Intra-priming 9 0.89
Reference redundancy Level 1.1 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 2337 -
5’ and 3’ reference supported (gene) 1563 66.88
5’ reference supported (gene) 1835 78.52
3’ reference supported (gene) 1978 84.64
5’ CAGE supported 1453 62.17
3’ polyA supported 2313 98.97
Supported Novel Transcript Model (SNTM) 1745 74.67
Intra-priming 11 0.47
Intron retention incidence 261 11.17

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 2859 -
5’ and 3’ reference supported (gene) 969 33.89
5’ reference supported (gene) 1600 55.96
3’ reference supported (gene) 1695 59.29
5’ CAGE supported 1725 60.34
3’ polyA supported 2821 98.67
Supported Novel Transcript Model (SNTM) 1138 39.8
Non-canonical SJ incidence 598 20.92
Full Illumina SJ support 1590 55.61
Intra-priming 12 0.42
RT-switching incidence 160 5.6

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 82
True Positive detections (TP) 80
SIRV transcripts associated to TP (Reference Match) 80
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 4
False Positive (FP) 2
Sensitivity 0.95
Precision 0.98
Non Redundant Precision 0.98
Positive Detection Rate 0.95
False Discovery Rate 0.02
False Detection Rate 0.02
Redundancy 1