Your submission: WTC11_R2C2only 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 13569
Number of known genes detected 12600
Number of transcripts detected 41048
Number of transcripts associated to a known gene 39574
Number of unique SJ detected 112583
Absolute value Relative value (%)
Novel SJ 3767 0.03
Non-canonical SJ 324 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 25147 -
Reference Match 10041 39.93
5’ reference supported (transcript) 18677 74.27
3’ reference supported (transcript) 13628 54.19
5’ reference supported (gene) 22487 89.42
3’ reference supported (gene) 19734 78.47
5’ CAGE supported 22160 88.12
3’ polyA supported 23629 93.96
Supported Reference Transcript Model (SRTM) 23122 91.95
Intra-priming 2238 8.9
Reference redundancy Level 1.42 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 3516 -
5’ reference supported (transcript) 1782 50.68
3’ reference supported (transcript) 985 28.01
5’ and 3’ reference supported (gene) 979 27.84
5’ reference supported (gene) 2450 2450
3’ reference supported (gene) 1760 50.06
5’ CAGE supported 2633 74.89
3’ polyA supported 2525 71.81
Supported Reference Transcript Model (SRTM) 1997 56.8
Intra-priming 1245 35.41
Reference redundancy Level 1.22 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 8911 -
5’ and 3’ reference supported (gene) 6636 74.47
5’ reference supported (gene) 8287 93
3’ reference supported (gene) 7112 79.81
5’ CAGE supported 7949 89.2
3’ polyA supported 7895 88.6
Supported Novel Transcript Model (SNTM) 6907 77.51
Intra-priming 1429 16.04
Intron retention incidence 2226 24.98

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 2000 -
5’ and 3’ reference supported (gene) 993 49.65
5’ reference supported (gene) 1469 73.45
3’ reference supported (gene) 1347 67.35
5’ CAGE supported 1673 83.65
3’ polyA supported 1842 92.1
Supported Novel Transcript Model (SNTM) 1258 62.9
Non-canonical SJ incidence 293 14.65
Full Illumina SJ support 1515 75.75
Intra-priming 252 12.6
RT-switching incidence 155 7.75

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 95
True Positive detections (TP) 70
SIRV transcripts associated to TP (Reference Match) 70
Partial True Positive detections (PTP) 9
SIRV transcripts associated to PTP 25
False Negative (FN) 5
False Positive (FP) 0
Sensitivity 0.83
Precision 0.74
Non Redundant Precision 0.74
Positive Detection Rate 0.94
False Discovery Rate 0.09
False Detection Rate 0
Redundancy 1.2