Your submission: H1_mix_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 16597
Number of known genes detected 16344
Number of transcripts detected 41769
Number of transcripts associated to a known gene 41487
Number of unique SJ detected 101597
Absolute value Relative value (%)
Novel SJ 649 0.01
Non-canonical SJ 56 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 40386 -
Reference Match 39867 98.71
5’ reference supported (transcript) 40081 99.24
3’ reference supported (transcript) 40075 99.23
5’ reference supported (gene) 40238 99.63
3’ reference supported (gene) 40173 99.47
5’ CAGE supported 23021 57
3’ polyA supported 30386 75.24
Supported Reference Transcript Model (SRTM) 40140 99.39
Intra-priming 1291 3.2
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 747 -
5’ reference supported (transcript) 159 21.29
3’ reference supported (transcript) 311 41.63
5’ and 3’ reference supported (gene) 100 13.39
5’ reference supported (gene) 269 269
3’ reference supported (gene) 462 61.85
5’ CAGE supported 247 33.07
3’ polyA supported 664 88.89
Supported Reference Transcript Model (SRTM) 264 35.34
Intra-priming 24 3.21
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 114 -
5’ and 3’ reference supported (gene) 75 65.79
5’ reference supported (gene) 100 87.72
3’ reference supported (gene) 87 76.32
5’ CAGE supported 86 75.44
3’ polyA supported 112 98.25
Supported Novel Transcript Model (SNTM) 85 74.56
Intra-priming 0 0
Intron retention incidence 16 14.04

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 240 -
5’ and 3’ reference supported (gene) 116 48.33
5’ reference supported (gene) 173 72.08
3’ reference supported (gene) 148 61.67
5’ CAGE supported 172 71.67
3’ polyA supported 237 98.75
Supported Novel Transcript Model (SNTM) 62 25.83
Non-canonical SJ incidence 13 5.42
Full Illumina SJ support 105 43.75
Intra-priming 3 1.25
RT-switching incidence 15 6.25

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 70
True Positive detections (TP) 69
SIRV transcripts associated to TP (Reference Match) 69
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 15
False Positive (FP) 1
Sensitivity 0.82
Precision 0.99
Non Redundant Precision 0.99
Positive Detection Rate 0.82
False Discovery Rate 0.01
False Detection Rate 0.01
Redundancy 1