Your submission: ES_R2C2_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 13936
Number of known genes detected 13583
Number of transcripts detected 26905
Number of transcripts associated to a known gene 26479
Number of unique SJ detected 121198
Absolute value Relative value (%)
Novel SJ 1689 0.01
Non-canonical SJ 78 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 24203 -
Reference Match 24201 99.99
5’ reference supported (transcript) 24201 99.99
3’ reference supported (transcript) 24203 100
5’ reference supported (gene) 24203 100
3’ reference supported (gene) 24203 100
5’ CAGE supported 370 1.53
3’ polyA supported 18081 74.71
Supported Reference Transcript Model (SRTM) 24203 100
Intra-priming 1916 7.92
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 753 -
5’ reference supported (transcript) 268 35.59
3’ reference supported (transcript) 271 35.99
5’ and 3’ reference supported (gene) 144 19.12
5’ reference supported (gene) 409 409
3’ reference supported (gene) 393 52.19
5’ CAGE supported 10 1.33
3’ polyA supported 603 80.08
Supported Reference Transcript Model (SRTM) 294 39.04
Intra-priming 30 3.98
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 651 -
5’ and 3’ reference supported (gene) 445 68.36
5’ reference supported (gene) 560 86.02
3’ reference supported (gene) 516 79.26
5’ CAGE supported 13 2
3’ polyA supported 588 90.32
Supported Novel Transcript Model (SNTM) 482 74.04
Intra-priming 6 0.92
Intron retention incidence 155 23.81

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 872 -
5’ and 3’ reference supported (gene) 431 49.43
5’ reference supported (gene) 592 67.89
3’ reference supported (gene) 624 71.56
5’ CAGE supported 14 1.61
3’ polyA supported 781 89.56
Supported Novel Transcript Model (SNTM) 134 15.37
Non-canonical SJ incidence 32 3.67
Full Illumina SJ support 320 36.7
Intra-priming 6 0.69
RT-switching incidence 139 15.94

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 68
True Positive detections (TP) 67
SIRV transcripts associated to TP (Reference Match) 67
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 17
False Positive (FP) 1
Sensitivity 0.8
Precision 0.99
Non Redundant Precision 0.99
Positive Detection Rate 0.8
False Discovery Rate 0.01
False Detection Rate 0.01
Redundancy 1