Your submission: WTC11_long_short 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 17492
Number of known genes detected 15819
Number of transcripts detected 44008
Number of transcripts associated to a known gene 41719
Number of unique SJ detected 140864
Absolute value Relative value (%)
Novel SJ 6848 0.05
Non-canonical SJ 1699 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 30980 -
Reference Match 22104 71.35
5’ reference supported (transcript) 25174 81.26
3’ reference supported (transcript) 25286 81.62
5’ reference supported (gene) 26583 85.81
3’ reference supported (gene) 26681 86.12
5’ CAGE supported 17205 55.54
3’ polyA supported 23930 77.24
Supported Reference Transcript Model (SRTM) 25307 81.69
Intra-priming 719 2.32
Reference redundancy Level 1.01 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1512 -
5’ reference supported (transcript) 382 25.26
3’ reference supported (transcript) 575 38.03
5’ and 3’ reference supported (gene) 426 28.17
5’ reference supported (gene) 697 697
3’ reference supported (gene) 951 62.9
5’ CAGE supported 566 37.43
3’ polyA supported 1222 80.82
Supported Reference Transcript Model (SRTM) 670 44.31
Intra-priming 25 1.65
Reference redundancy Level 1.08 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 4975 -
5’ and 3’ reference supported (gene) 3469 69.73
5’ reference supported (gene) 4050 81.41
3’ reference supported (gene) 4189 84.2
5’ CAGE supported 3494 70.23
3’ polyA supported 4676 93.99
Supported Novel Transcript Model (SNTM) 3704 74.45
Intra-priming 58 1.17
Intron retention incidence 982 19.74

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 4252 -
5’ and 3’ reference supported (gene) 1234 29.02
5’ reference supported (gene) 2884 67.83
3’ reference supported (gene) 1952 45.91
5’ CAGE supported 2764 65
3’ polyA supported 3170 74.55
Supported Novel Transcript Model (SNTM) 1687 39.68
Non-canonical SJ incidence 1585 37.28
Full Illumina SJ support 2481 58.35
Intra-priming 172 4.05
RT-switching incidence 380 8.94

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 88
True Positive detections (TP) 73
SIRV transcripts associated to TP (Reference Match) 73
Partial True Positive detections (PTP) 1
SIRV transcripts associated to PTP 1
False Negative (FN) 10
False Positive (FP) 14
Sensitivity 0.87
Precision 0.83
Non Redundant Precision 0.83
Positive Detection Rate 0.88
False Discovery Rate 0.17
False Detection Rate 0.16
Redundancy 1