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 8155
Number of known genes detected 8100
Number of transcripts detected 28396
Number of transcripts associated to a known gene 27070
Number of unique SJ detected 69802
Absolute value Relative value (%)
Novel SJ 7420 0.11
Non-canonical SJ 12260 0.18

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 14844 -
Reference Match 11383 76.68
5’ reference supported (transcript) 13685 92.19
3’ reference supported (transcript) 11907 80.21
5’ reference supported (gene) 14533 97.9
3’ reference supported (gene) 13605 91.65
5’ CAGE supported 11614 78.24
3’ polyA supported 13986 94.22
Supported Reference Transcript Model (SRTM) 14499 97.68
Intra-priming 305 2.05
Reference redundancy Level 1.12 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1569 -
5’ reference supported (transcript) 729 46.46
3’ reference supported (transcript) 460 29.32
5’ and 3’ reference supported (gene) 436 27.79
5’ reference supported (gene) 1031 1031
3’ reference supported (gene) 863 55
5’ CAGE supported 1064 67.81
3’ polyA supported 1348 85.91
Supported Reference Transcript Model (SRTM) 1033 65.84
Intra-priming 126 8.03
Reference redundancy Level 1.12 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 4323 -
5’ and 3’ reference supported (gene) 2082 48.16
5’ reference supported (gene) 2419 55.96
3’ reference supported (gene) 2206 51.03
5’ CAGE supported 2172 50.24
3’ polyA supported 2518 58.25
Supported Novel Transcript Model (SNTM) 2081 48.14
Intra-priming 41 0.95
Intron retention incidence 522 12.07

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 6334 -
5’ and 3’ reference supported (gene) 4259 67.24
5’ reference supported (gene) 5270 83.2
3’ reference supported (gene) 4730 74.68
5’ CAGE supported 5131 81.01
3’ polyA supported 5805 91.65
Supported Novel Transcript Model (SNTM) 1583 24.99
Non-canonical SJ incidence 1184 18.69
Full Illumina SJ support 1777 28.05
Intra-priming 85 1.34
RT-switching incidence 210 3.32

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 119
True Positive detections (TP) 62
SIRV transcripts associated to TP (Reference Match) 62
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 2
False Negative (FN) 22
False Positive (FP) 55
Sensitivity 0.74
Precision 0.52
Non Redundant Precision 0.52
Positive Detection Rate 0.74
False Discovery Rate 0.46
False Detection Rate 0.46
Redundancy 1.03