Your submission: WTC11_cdna_ont_ls on ONT+Illumina 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 19504
Number of known genes detected 13226
Number of transcripts detected 49045
Number of transcripts associated to a known gene 41986
Number of unique SJ detected 92623
Absolute value Relative value (%)
Novel SJ 8428 0.09
Non-canonical SJ 310 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 26584 -
Reference Match 19901 74.86
5’ reference supported (transcript) 24161 90.89
3’ reference supported (transcript) 20694 77.84
5’ reference supported (gene) 25419 95.62
3’ reference supported (gene) 23877 89.82
5’ CAGE supported 18159 68.31
3’ polyA supported 23624 88.87
Supported Reference Transcript Model (SRTM) 25560 96.15
Intra-priming 537 2.02
Reference redundancy Level 1.1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2589 -
5’ reference supported (transcript) 358 13.83
3’ reference supported (transcript) 1233 47.62
5’ and 3’ reference supported (gene) 262 10.12
5’ reference supported (gene) 574 574
3’ reference supported (gene) 1591 61.45
5’ CAGE supported 634 24.49
3’ polyA supported 2405 92.89
Supported Reference Transcript Model (SRTM) 675 26.07
Intra-priming 25 0.97
Reference redundancy Level 1.11 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 9208 -
5’ and 3’ reference supported (gene) 7286 79.13
5’ reference supported (gene) 8524 92.57
3’ reference supported (gene) 7737 84.02
5’ CAGE supported 8069 87.63
3’ polyA supported 9075 98.56
Supported Novel Transcript Model (SNTM) 6769 73.51
Intra-priming 47 0.51
Intron retention incidence 1168 12.68

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 3605 -
5’ and 3’ reference supported (gene) 1838 50.98
5’ reference supported (gene) 2704 75.01
3’ reference supported (gene) 2399 66.55
5’ CAGE supported 3034 84.16
3’ polyA supported 3577 99.22
Supported Novel Transcript Model (SNTM) 2897 80.36
Non-canonical SJ incidence 139 3.86
Full Illumina SJ support 3224 89.43
Intra-priming 15 0.42
RT-switching incidence 193 5.35

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 105
True Positive detections (TP) 76
SIRV transcripts associated to TP (Reference Match) 76
Partial True Positive detections (PTP) 4
SIRV transcripts associated to PTP 5
False Negative (FN) 4
False Positive (FP) 24
Sensitivity 0.9
Precision 0.72
Non Redundant Precision 0.72
Positive Detection Rate 0.95
False Discovery Rate 0.27
False Detection Rate 0.23
Redundancy 1.01