Your submission: WTC11_drna_ont_ls on ONT+Illumina 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 8534
Number of known genes detected 8463
Number of transcripts detected 14371
Number of transcripts associated to a known gene 14240
Number of unique SJ detected 60221
Absolute value Relative value (%)
Novel SJ 577 0.01
Non-canonical SJ 138 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 12789 -
Reference Match 9679 75.68
5’ reference supported (transcript) 12045 94.18
3’ reference supported (transcript) 9933 77.67
5’ reference supported (gene) 12557 98.19
3’ reference supported (gene) 11562 90.41
5’ CAGE supported 9664 75.56
3’ polyA supported 12120 94.77
Supported Reference Transcript Model (SRTM) 12625 98.72
Intra-priming 152 1.19
Reference redundancy Level 1.07 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 458 -
5’ reference supported (transcript) 31 6.77
3’ reference supported (transcript) 249 54.37
5’ and 3’ reference supported (gene) 76 16.59
5’ reference supported (gene) 107 107
3’ reference supported (gene) 332 72.49
5’ CAGE supported 101 22.05
3’ polyA supported 435 94.98
Supported Reference Transcript Model (SRTM) 140 30.57
Intra-priming 3 0.66
Reference redundancy Level 1.03 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 689 -
5’ and 3’ reference supported (gene) 539 78.23
5’ reference supported (gene) 624 90.57
3’ reference supported (gene) 581 84.33
5’ CAGE supported 571 82.87
3’ polyA supported 677 98.26
Supported Novel Transcript Model (SNTM) 527 76.49
Intra-priming 3 0.44
Intron retention incidence 87 12.63

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 304 -
5’ and 3’ reference supported (gene) 151 49.67
5’ reference supported (gene) 237 77.96
3’ reference supported (gene) 197 64.8
5’ CAGE supported 232 76.32
3’ polyA supported 302 99.34
Supported Novel Transcript Model (SNTM) 225 74.01
Non-canonical SJ incidence 52 17.11
Full Illumina SJ support 246 80.92
Intra-priming 3 0.99
RT-switching incidence 51 16.78

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) 75
SIRV transcripts associated to TP (Reference Match) 75
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 9
False Positive (FP) 2
Sensitivity 0.89
Precision 0.97
Non Redundant Precision 0.97
Positive Detection Rate 0.89
False Discovery Rate 0.03
False Detection Rate 0.03
Redundancy 1