Your submission: H1_mix_dRNA_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 518
Number of known genes detected 509
Number of transcripts detected 607
Number of transcripts associated to a known gene 596
Number of unique SJ detected 3086
Absolute value Relative value (%)
Novel SJ 186 0.06
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 362 -
Reference Match 238 65.75
5’ reference supported (transcript) 311 85.91
3’ reference supported (transcript) 274 75.69
5’ reference supported (gene) 355 98.07
3’ reference supported (gene) 331 91.44
5’ CAGE supported 251 69.34
3’ polyA supported 362 100
Supported Reference Transcript Model (SRTM) 357 98.62
Intra-priming 0 0
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 38 -
5’ reference supported (transcript) 3 7.89
3’ reference supported (transcript) 25 65.79
5’ and 3’ reference supported (gene) 15 39.47
5’ reference supported (gene) 15 15
3’ reference supported (gene) 34 89.47
5’ CAGE supported 6 15.79
3’ polyA supported 38 100
Supported Reference Transcript Model (SRTM) 18 47.37
Intra-priming 0 0
Reference redundancy Level 1 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 42 -
5’ and 3’ reference supported (gene) 32 76.19
5’ reference supported (gene) 35 83.33
3’ reference supported (gene) 37 88.1
5’ CAGE supported 23 54.76
3’ polyA supported 42 100
Supported Novel Transcript Model (SNTM) 30 71.43
Intra-priming 0 0
Intron retention incidence 4 9.52

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 154 -
5’ and 3’ reference supported (gene) 131 85.06
5’ reference supported (gene) 138 89.61
3’ reference supported (gene) 142 92.21
5’ CAGE supported 68 44.16
3’ polyA supported 152 98.7
Supported Novel Transcript Model (SNTM) 32 20.78
Non-canonical SJ incidence 0 0
Full Illumina SJ support 37 24.03
Intra-priming 0 0
RT-switching incidence 12 7.79

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 63
True Positive detections (TP) 23
SIRV transcripts associated to TP (Reference Match) 23
Partial True Positive detections (PTP) 1
SIRV transcripts associated to PTP 1
False Negative (FN) 60
False Positive (FP) 39
Sensitivity 0.27
Precision 0.37
Non Redundant Precision 0.37
Positive Detection Rate 0.29
False Discovery Rate 0.63
False Detection Rate 0.62
Redundancy 1