Your submission: ES_drna_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 11677
Number of known genes detected 11669
Number of transcripts detected 18410
Number of transcripts associated to a known gene 18355
Number of unique SJ detected 113606
Absolute value Relative value (%)
Novel SJ 848 0.01
Non-canonical SJ 205 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 16895 -
Reference Match 16894 99.99
5’ reference supported (transcript) 16894 99.99
3’ reference supported (transcript) 16895 100
5’ reference supported (gene) 16894 99.99
3’ reference supported (gene) 16895 100
5’ CAGE supported 282 1.67
3’ polyA supported 14411 85.3
Supported Reference Transcript Model (SRTM) 16894 99.99
Intra-priming 568 3.36
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 159 -
5’ reference supported (transcript) 39 24.53
3’ reference supported (transcript) 75 47.17
5’ and 3’ reference supported (gene) 40 25.16
5’ reference supported (gene) 69 69
3’ reference supported (gene) 107 67.3
5’ CAGE supported 0 0
3’ polyA supported 141 88.68
Supported Reference Transcript Model (SRTM) 61 38.36
Intra-priming 3 1.89
Reference redundancy Level 1.01 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 752 -
5’ and 3’ reference supported (gene) 507 67.42
5’ reference supported (gene) 594 78.99
3’ reference supported (gene) 646 85.9
5’ CAGE supported 17 2.26
3’ polyA supported 706 93.88
Supported Novel Transcript Model (SNTM) 531 70.61
Intra-priming 8 1.06
Intron retention incidence 94 12.5

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 549 -
5’ and 3’ reference supported (gene) 192 34.97
5’ reference supported (gene) 287 52.28
3’ reference supported (gene) 364 66.3
5’ CAGE supported 3 0.55
3’ polyA supported 472 85.97
Supported Novel Transcript Model (SNTM) 145 26.41
Non-canonical SJ incidence 96 17.49
Full Illumina SJ support 358 65.21
Intra-priming 4 0.73
RT-switching incidence 76 13.84

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 77
True Positive detections (TP) 75
SIRV transcripts associated to TP (Reference Match) 75
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 9
False Positive (FP) 2
Sensitivity 0.89
Precision 0.97
Non Redundant Precision 0.97
Positive Detection Rate 0.89
False Discovery Rate 0.03
False Detection Rate 0.03
Redundancy 1