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 6589
Number of known genes detected 6589
Number of transcripts detected 12831
Number of transcripts associated to a known gene 12820
Number of unique SJ detected 61481
Absolute value Relative value (%)
Novel SJ 1190 0.02
Non-canonical SJ 350 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 10851 -
Reference Match 6521 60.1
5’ reference supported (transcript) 8550 78.79
3’ reference supported (transcript) 7586 69.91
5’ reference supported (gene) 10353 95.41
3’ reference supported (gene) 9048 83.38
5’ CAGE supported 193 1.78
3’ polyA supported 10497 96.74
Supported Reference Transcript Model (SRTM) 10186 93.87
Intra-priming 132 1.22
Reference redundancy Level 1.24 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 358 -
5’ reference supported (transcript) 51 14.25
3’ reference supported (transcript) 235 65.64
5’ and 3’ reference supported (gene) 99 27.65
5’ reference supported (gene) 130 130
3’ reference supported (gene) 297 82.96
5’ CAGE supported 2 0.56
3’ polyA supported 342 95.53
Supported Reference Transcript Model (SRTM) 120 33.52
Intra-priming 1 0.28
Reference redundancy Level 1.13 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 466 -
5’ and 3’ reference supported (gene) 392 84.12
5’ reference supported (gene) 441 94.64
3’ reference supported (gene) 414 88.84
5’ CAGE supported 8 1.72
3’ polyA supported 455 97.64
Supported Novel Transcript Model (SNTM) 384 82.4
Intra-priming 1 0.21
Intron retention incidence 51 10.94

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 1145 -
5’ and 3’ reference supported (gene) 768 67.07
5’ reference supported (gene) 936 81.75
3’ reference supported (gene) 923 80.61
5’ CAGE supported 15 1.31
3’ polyA supported 1116 97.47
Supported Novel Transcript Model (SNTM) 190 16.59
Non-canonical SJ incidence 317 27.69
Full Illumina SJ support 292 25.5
Intra-priming 7 0.61
RT-switching incidence 133 11.62

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 76
True Positive detections (TP) 66
SIRV transcripts associated to TP (Reference Match) 66
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 3
False Negative (FN) 18
False Positive (FP) 7
Sensitivity 0.79
Precision 0.87
Non Redundant Precision 0.87
Positive Detection Rate 0.79
False Discovery Rate 0.09
False Detection Rate 0.09
Redundancy 1.05