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 16885
Number of known genes detected 16581
Number of transcripts detected 45300
Number of transcripts associated to a known gene 44463
Number of unique SJ detected 152151
Absolute value Relative value (%)
Novel SJ 5137 0.03
Non-canonical SJ 824 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 37122 -
Reference Match 36550 98.46
5’ reference supported (transcript) 36761 99.03
3’ reference supported (transcript) 36804 99.14
5’ reference supported (gene) 36957 99.56
3’ reference supported (gene) 36937 99.5
5’ CAGE supported 24947 67.2
3’ polyA supported 31051 83.65
Supported Reference Transcript Model (SRTM) 36882 99.35
Intra-priming 841 2.27
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1194 -
5’ reference supported (transcript) 449 37.6
3’ reference supported (transcript) 227 19.01
5’ and 3’ reference supported (gene) 275 23.03
5’ reference supported (gene) 736 736
3’ reference supported (gene) 538 45.06
5’ CAGE supported 394 33
3’ polyA supported 1103 92.38
Supported Reference Transcript Model (SRTM) 728 60.97
Intra-priming 11 0.92
Reference redundancy Level 1.1 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 2946 -
5’ and 3’ reference supported (gene) 1930 65.51
5’ reference supported (gene) 2235 75.87
3’ reference supported (gene) 2536 86.08
5’ CAGE supported 1110 37.68
3’ polyA supported 2916 98.98
Supported Novel Transcript Model (SNTM) 2046 69.45
Intra-priming 13 0.44
Intron retention incidence 357 12.12

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 3201 -
5’ and 3’ reference supported (gene) 997 31.15
5’ reference supported (gene) 1730 54.05
3’ reference supported (gene) 1855 57.95
5’ CAGE supported 966 30.18
3’ polyA supported 3139 98.06
Supported Novel Transcript Model (SNTM) 986 30.8
Non-canonical SJ incidence 644 20.12
Full Illumina SJ support 1872 58.48
Intra-priming 12 0.37
RT-switching incidence 196 6.12

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 82
True Positive detections (TP) 79
SIRV transcripts associated to TP (Reference Match) 79
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 1
False Negative (FN) 5
False Positive (FP) 2
Sensitivity 0.94
Precision 0.96
Non Redundant Precision 0.96
Positive Detection Rate 0.94
False Discovery Rate 0.02
False Detection Rate 0.02
Redundancy 1.01