Your submission: WTC11_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 18094
Number of known genes detected 17640
Number of transcripts detected 46449
Number of transcripts associated to a known gene 45911
Number of unique SJ detected 122981
Absolute value Relative value (%)
Novel SJ 1143 0.01
Non-canonical SJ 130 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 44420 -
Reference Match 43884 98.79
5’ reference supported (transcript) 44102 99.28
3’ reference supported (transcript) 44099 99.28
5’ reference supported (gene) 44265 99.65
3’ reference supported (gene) 44209 99.52
5’ CAGE supported 26266 59.13
3’ polyA supported 33705 75.88
Supported Reference Transcript Model (SRTM) 44188 99.48
Intra-priming 1368 3.08
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 780 -
5’ reference supported (transcript) 193 24.74
3’ reference supported (transcript) 345 44.23
5’ and 3’ reference supported (gene) 139 17.82
5’ reference supported (gene) 346 346
3’ reference supported (gene) 477 61.15
5’ CAGE supported 373 47.82
3’ polyA supported 661 84.74
Supported Reference Transcript Model (SRTM) 370 47.44
Intra-priming 6 0.77
Reference redundancy Level 1.04 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 401 -
5’ and 3’ reference supported (gene) 279 69.58
5’ reference supported (gene) 361 90.02
3’ reference supported (gene) 310 77.31
5’ CAGE supported 354 88.28
3’ polyA supported 388 96.76
Supported Novel Transcript Model (SNTM) 305 76.06
Intra-priming 2 0.5
Intron retention incidence 42 10.47

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 310 -
5’ and 3’ reference supported (gene) 79 25.48
5’ reference supported (gene) 180 58.06
3’ reference supported (gene) 136 43.87
5’ CAGE supported 255 82.26
3’ polyA supported 294 94.84
Supported Novel Transcript Model (SNTM) 212 68.39
Non-canonical SJ incidence 24 7.74
Full Illumina SJ support 252 81.29
Intra-priming 1 0.32
RT-switching incidence 12 3.87

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 80
True Positive detections (TP) 79
SIRV transcripts associated to TP (Reference Match) 79
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 5
False Positive (FP) 1
Sensitivity 0.94
Precision 0.99
Non Redundant Precision 0.99
Positive Detection Rate 0.94
False Discovery Rate 0.01
False Detection Rate 0.01
Redundancy 1