Your submission: WTC11_r2c2_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 14195
Number of known genes detected 14153
Number of transcripts detected 41040
Number of transcripts associated to a known gene 40881
Number of unique SJ detected 143739
Absolute value Relative value (%)
Novel SJ 2630 0.02
Non-canonical SJ 480 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 31376 -
Reference Match 30934 98.59
5’ reference supported (transcript) 31097 99.11
3’ reference supported (transcript) 31108 99.15
5’ reference supported (gene) 31254 99.61
3’ reference supported (gene) 31210 99.47
5’ CAGE supported 23856 76.03
3’ polyA supported 26101 83.19
Supported Reference Transcript Model (SRTM) 31208 99.46
Intra-priming 916 2.92
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 3502 -
5’ reference supported (transcript) 1600 45.69
3’ reference supported (transcript) 194 5.54
5’ and 3’ reference supported (gene) 632 18.05
5’ reference supported (gene) 2388 2388
3’ reference supported (gene) 917 26.19
5’ CAGE supported 2132 60.88
3’ polyA supported 2820 80.53
Supported Reference Transcript Model (SRTM) 2145 61.25
Intra-priming 335 9.57
Reference redundancy Level 1.47 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 4216 -
5’ and 3’ reference supported (gene) 2656 63
5’ reference supported (gene) 3213 76.21
3’ reference supported (gene) 3444 81.69
5’ CAGE supported 2571 60.98
3’ polyA supported 4078 96.73
Supported Novel Transcript Model (SNTM) 3154 74.81
Intra-priming 158 3.75
Intron retention incidence 1001 23.74

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 1787 -
5’ and 3’ reference supported (gene) 771 43.14
5’ reference supported (gene) 1113 62.28
3’ reference supported (gene) 1213 67.88
5’ CAGE supported 1140 63.79
3’ polyA supported 1707 95.52
Supported Novel Transcript Model (SNTM) 876 49.02
Non-canonical SJ incidence 361 20.2
Full Illumina SJ support 1186 66.37
Intra-priming 64 3.58
RT-switching incidence 166 9.29

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) 78
SIRV transcripts associated to TP (Reference Match) 78
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 2
False Negative (FN) 6
False Positive (FP) 2
Sensitivity 0.93
Precision 0.95
Non Redundant Precision 0.95
Positive Detection Rate 0.93
False Discovery Rate 0.02
False Detection Rate 0.02
Redundancy 1.03