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 12971
Number of known genes detected 12954
Number of transcripts detected 30866
Number of transcripts associated to a known gene 30725
Number of unique SJ detected 129576
Absolute value Relative value (%)
Novel SJ 2712 0.02
Non-canonical SJ 435 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 22429 -
Reference Match 22426 99.99
5’ reference supported (transcript) 22426 99.99
3’ reference supported (transcript) 22429 100
5’ reference supported (gene) 22426 99.99
3’ reference supported (gene) 22429 100
5’ CAGE supported 378 1.69
3’ polyA supported 17546 78.23
Supported Reference Transcript Model (SRTM) 22426 99.99
Intra-priming 1847 8.23
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2904 -
5’ reference supported (transcript) 1346 46.35
3’ reference supported (transcript) 209 7.2
5’ and 3’ reference supported (gene) 441 15.19
5’ reference supported (gene) 1885 1885
3’ reference supported (gene) 747 25.72
5’ CAGE supported 35 1.21
3’ polyA supported 1992 68.6
Supported Reference Transcript Model (SRTM) 1296 44.63
Intra-priming 273 9.4
Reference redundancy Level 1.5 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 3329 -
5’ and 3’ reference supported (gene) 1895 56.92
5’ reference supported (gene) 2405 72.24
3’ reference supported (gene) 2617 78.61
5’ CAGE supported 24 0.72
3’ polyA supported 3002 90.18
Supported Novel Transcript Model (SNTM) 2092 62.84
Intra-priming 129 3.88
Intron retention incidence 635 19.07

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 2063 -
5’ and 3’ reference supported (gene) 696 33.74
5’ reference supported (gene) 1017 49.3
3’ reference supported (gene) 1440 69.8
5’ CAGE supported 11 0.53
3’ polyA supported 1828 88.61
Supported Novel Transcript Model (SNTM) 599 29.04
Non-canonical SJ incidence 300 14.54
Full Illumina SJ support 1452 70.38
Intra-priming 77 3.73
RT-switching incidence 210 10.18

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) 76
SIRV transcripts associated to TP (Reference Match) 76
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 2
False Negative (FN) 8
False Positive (FP) 3
Sensitivity 0.9
Precision 0.94
Non Redundant Precision 0.94
Positive Detection Rate 0.9
False Discovery Rate 0.04
False Detection Rate 0.04
Redundancy 1.03