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 3464
Number of known genes detected 2790
Number of transcripts detected 6599
Number of transcripts associated to a known gene 5397
Number of unique SJ detected 14960
Absolute value Relative value (%)
Novel SJ 3625 0.24
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 1464 -
Reference Match 780 53.28
5’ reference supported (transcript) 1122 76.64
3’ reference supported (transcript) 983 67.14
5’ reference supported (gene) 1299 88.73
3’ reference supported (gene) 1249 85.31
5’ CAGE supported 1113 76.02
3’ polyA supported 1413 96.52
Supported Reference Transcript Model (SRTM) 1339 91.46
Intra-priming 2 0.14
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 387 -
5’ reference supported (transcript) 84 21.71
3’ reference supported (transcript) 203 52.45
5’ and 3’ reference supported (gene) 73 18.86
5’ reference supported (gene) 126 126
3’ reference supported (gene) 290 74.94
5’ CAGE supported 124 32.04
3’ polyA supported 361 93.28
Supported Reference Transcript Model (SRTM) 131 33.85
Intra-priming 0 0
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 990 -
5’ and 3’ reference supported (gene) 539 54.44
5’ reference supported (gene) 580 58.59
3’ reference supported (gene) 903 91.21
5’ CAGE supported 562 56.77
3’ polyA supported 987 99.7
Supported Novel Transcript Model (SNTM) 476 48.08
Intra-priming 0 0
Intron retention incidence 97 9.8

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 2556 -
5’ and 3’ reference supported (gene) 2072 81.06
5’ reference supported (gene) 2301 90.02
3’ reference supported (gene) 2208 86.38
5’ CAGE supported 2269 88.77
3’ polyA supported 2509 98.16
Supported Novel Transcript Model (SNTM) 605 23.67
Non-canonical SJ incidence 0 0
Full Illumina SJ support 671 26.25
Intra-priming 0 0
RT-switching incidence 101 3.95

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 312
True Positive detections (TP) 20
SIRV transcripts associated to TP (Reference Match) 20
Partial True Positive detections (PTP) 2
SIRV transcripts associated to PTP 2
False Negative (FN) 62
False Positive (FP) 290
Sensitivity 0.24
Precision 0.06
Non Redundant Precision 0.06
Positive Detection Rate 0.26
False Discovery Rate 0.94
False Detection Rate 0.93
Redundancy 1