Your submission: H1_mix_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 4218
Number of known genes detected 4101
Number of transcripts detected 6604
Number of transcripts associated to a known gene 6434
Number of unique SJ detected 36146
Absolute value Relative value (%)
Novel SJ 1275 0.04
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 3851 -
Reference Match 2009 52.17
5’ reference supported (transcript) 3013 78.24
3’ reference supported (transcript) 2571 66.76
5’ reference supported (gene) 3574 92.81
3’ reference supported (gene) 3337 86.65
5’ CAGE supported 3031 78.71
3’ polyA supported 3735 96.99
Supported Reference Transcript Model (SRTM) 3639 94.49
Intra-priming 7 0.18
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 418 -
5’ reference supported (transcript) 244 58.37
3’ reference supported (transcript) 135 32.3
5’ and 3’ reference supported (gene) 148 35.41
5’ reference supported (gene) 319 319
3’ reference supported (gene) 227 54.31
5’ CAGE supported 304 72.73
3’ polyA supported 344 82.3
Supported Reference Transcript Model (SRTM) 276 66.03
Intra-priming 4 0.96
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1150 -
5’ and 3’ reference supported (gene) 955 83.04
5’ reference supported (gene) 1098 95.48
3’ reference supported (gene) 995 86.52
5’ CAGE supported 1011 87.91
3’ polyA supported 1107 96.26
Supported Novel Transcript Model (SNTM) 982 85.39
Intra-priming 2 0.17
Intron retention incidence 400 34.78

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 1015 -
5’ and 3’ reference supported (gene) 809 79.7
5’ reference supported (gene) 921 90.74
3’ reference supported (gene) 876 86.31
5’ CAGE supported 880 86.7
3’ polyA supported 996 98.13
Supported Novel Transcript Model (SNTM) 371 36.55
Non-canonical SJ incidence 0 0
Full Illumina SJ support 413 40.69
Intra-priming 1 0.1
RT-switching incidence 91 8.97

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 77
True Positive detections (TP) 47
SIRV transcripts associated to TP (Reference Match) 47
Partial True Positive detections (PTP) 6
SIRV transcripts associated to PTP 6
False Negative (FN) 31
False Positive (FP) 24
Sensitivity 0.56
Precision 0.61
Non Redundant Precision 0.61
Positive Detection Rate 0.63
False Discovery Rate 0.39
False Detection Rate 0.31
Redundancy 1