Your submission: WTC11_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 8690
Number of known genes detected 8673
Number of transcripts detected 14449
Number of transcripts associated to a known gene 14397
Number of unique SJ detected 58907
Absolute value Relative value (%)
Novel SJ 228 0
Non-canonical SJ 139 0

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 11526 -
Reference Match 9593 83.23
5’ reference supported (transcript) 10970 95.18
3’ reference supported (transcript) 9818 85.18
5’ reference supported (gene) 11301 98.05
3’ reference supported (gene) 10776 93.49
5’ CAGE supported 8333 72.3
3’ polyA supported 10859 94.21
Supported Reference Transcript Model (SRTM) 11284 97.9
Intra-priming 152 1.32
Reference redundancy Level 1.04 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2234 -
5’ reference supported (transcript) 25 1.12
3’ reference supported (transcript) 1154 51.66
5’ and 3’ reference supported (gene) 265 11.86
5’ reference supported (gene) 329 329
3’ reference supported (gene) 1693 75.78
5’ CAGE supported 177 7.92
3’ polyA supported 2163 96.82
Supported Reference Transcript Model (SRTM) 417 18.67
Intra-priming 15 0.67
Reference redundancy Level 1.01 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 582 -
5’ and 3’ reference supported (gene) 343 58.93
5’ reference supported (gene) 401 68.9
3’ reference supported (gene) 471 80.93
5’ CAGE supported 344 59.11
3’ polyA supported 573 98.45
Supported Novel Transcript Model (SNTM) 330 56.7
Intra-priming 1 0.17
Intron retention incidence 64 11

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 55 -
5’ and 3’ reference supported (gene) 25 45.45
5’ reference supported (gene) 31 56.36
3’ reference supported (gene) 45 81.82
5’ CAGE supported 32 58.18
3’ polyA supported 54 98.18
Supported Novel Transcript Model (SNTM) 1 1.82
Non-canonical SJ incidence 53 96.36
Full Illumina SJ support 1 1.82
Intra-priming 2 3.64
RT-switching incidence 41 74.55

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