Your submission: H1_mix_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 19632
Number of known genes detected 14288
Number of transcripts detected 48565
Number of transcripts associated to a known gene 42684
Number of unique SJ detected 100406
Absolute value Relative value (%)
Novel SJ 4287 0.04
Non-canonical SJ 331 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 29990 -
Reference Match 22586 75.31
5’ reference supported (transcript) 27585 91.98
3’ reference supported (transcript) 23344 77.84
5’ reference supported (gene) 28951 96.54
3’ reference supported (gene) 26934 89.81
5’ CAGE supported 20017 66.75
3’ polyA supported 26681 88.97
Supported Reference Transcript Model (SRTM) 29039 96.83
Intra-priming 532 1.77
Reference redundancy Level 1.1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2338 -
5’ reference supported (transcript) 377 16.12
3’ reference supported (transcript) 1056 45.17
5’ and 3’ reference supported (gene) 279 11.93
5’ reference supported (gene) 596 596
3’ reference supported (gene) 1378 58.94
5’ CAGE supported 571 24.42
3’ polyA supported 2170 92.81
Supported Reference Transcript Model (SRTM) 637 27.25
Intra-priming 31 1.33
Reference redundancy Level 1.11 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 10228 -
5’ and 3’ reference supported (gene) 8027 78.48
5’ reference supported (gene) 9436 92.26
3’ reference supported (gene) 8571 83.8
5’ CAGE supported 8330 81.44
3’ polyA supported 10092 98.67
Supported Novel Transcript Model (SNTM) 7358 71.94
Intra-priming 83 0.81
Intron retention incidence 1332 13.02

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 128 -
5’ and 3’ reference supported (gene) 60 46.88
5’ reference supported (gene) 81 63.28
3’ reference supported (gene) 96 75
5’ CAGE supported 60 46.88
3’ polyA supported 120 93.75
Supported Novel Transcript Model (SNTM) 1 0.78
Non-canonical SJ incidence 123 96.09
Full Illumina SJ support 1 0.78
Intra-priming 4 3.12
RT-switching incidence 67 52.34

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 108
True Positive detections (TP) 74
SIRV transcripts associated to TP (Reference Match) 74
Partial True Positive detections (PTP) 4
SIRV transcripts associated to PTP 6
False Negative (FN) 6
False Positive (FP) 28
Sensitivity 0.88
Precision 0.69
Non Redundant Precision 0.69
Positive Detection Rate 0.93
False Discovery Rate 0.3
False Detection Rate 0.26
Redundancy 1.03