Your submission: ES_cdna_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 14011
Number of known genes detected 13780
Number of transcripts detected 28289
Number of transcripts associated to a known gene 27550
Number of unique SJ detected 120177
Absolute value Relative value (%)
Novel SJ 4266 0.04
Non-canonical SJ 772 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 22361 -
Reference Match 22358 99.99
5’ reference supported (transcript) 22359 99.99
3’ reference supported (transcript) 22360 100
5’ reference supported (gene) 22359 99.99
3’ reference supported (gene) 22361 100
5’ CAGE supported 350 1.57
3’ polyA supported 17472 78.14
Supported Reference Transcript Model (SRTM) 22359 99.99
Intra-priming 1053 4.71
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 835 -
5’ reference supported (transcript) 256 30.66
3’ reference supported (transcript) 264 31.62
5’ and 3’ reference supported (gene) 118 14.13
5’ reference supported (gene) 380 380
3’ reference supported (gene) 407 48.74
5’ CAGE supported 13 1.56
3’ polyA supported 685 82.04
Supported Reference Transcript Model (SRTM) 308 36.89
Intra-priming 12 1.44
Reference redundancy Level 1.11 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1763 -
5’ and 3’ reference supported (gene) 1111 63.02
5’ reference supported (gene) 1310 74.31
3’ reference supported (gene) 1479 83.89
5’ CAGE supported 26 1.47
3’ polyA supported 1657 93.99
Supported Novel Transcript Model (SNTM) 1163 65.97
Intra-priming 8 0.45
Intron retention incidence 221 12.54

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 2591 -
5’ and 3’ reference supported (gene) 662 25.55
5’ reference supported (gene) 1111 42.88
3’ reference supported (gene) 1582 61.06
5’ CAGE supported 14 0.54
3’ polyA supported 2142 82.67
Supported Novel Transcript Model (SNTM) 477 18.41
Non-canonical SJ incidence 447 17.25
Full Illumina SJ support 1575 60.79
Intra-priming 21 0.81
RT-switching incidence 203 7.83

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 81
True Positive detections (TP) 79
SIRV transcripts associated to TP (Reference Match) 79
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 1
False Negative (FN) 5
False Positive (FP) 1
Sensitivity 0.94
Precision 0.98
Non Redundant Precision 0.98
Positive Detection Rate 0.94
False Discovery Rate 0.01
False Detection Rate 0.01
Redundancy 1.01