Your submission: ES_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 8409
Number of known genes detected 8351
Number of transcripts detected 24992
Number of transcripts associated to a known gene 24110
Number of unique SJ detected 79871
Absolute value Relative value (%)
Novel SJ 5787 0.07
Non-canonical SJ 10911 0.14

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 15408 -
Reference Match 10116 65.65
5’ reference supported (transcript) 12951 84.05
3’ reference supported (transcript) 11089 71.97
5’ reference supported (gene) 14778 95.91
3’ reference supported (gene) 12820 83.2
5’ CAGE supported 264 1.71
3’ polyA supported 13604 88.29
Supported Reference Transcript Model (SRTM) 14052 91.2
Intra-priming 275 1.78
Reference redundancy Level 1.29 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1047 -
5’ reference supported (transcript) 375 35.82
3’ reference supported (transcript) 405 38.68
5’ and 3’ reference supported (gene) 216 20.63
5’ reference supported (gene) 569 569
3’ reference supported (gene) 591 56.45
5’ CAGE supported 9 0.86
3’ polyA supported 772 73.73
Supported Reference Transcript Model (SRTM) 354 33.81
Intra-priming 13 1.24
Reference redundancy Level 1.15 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 2614 -
5’ and 3’ reference supported (gene) 1351 51.68
5’ reference supported (gene) 1681 64.31
3’ reference supported (gene) 1438 55.01
5’ CAGE supported 33 1.26
3’ polyA supported 1691 64.69
Supported Novel Transcript Model (SNTM) 1440 55.09
Intra-priming 7 0.27
Intron retention incidence 413 15.8

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 5041 -
5’ and 3’ reference supported (gene) 2709 53.74
5’ reference supported (gene) 3524 69.91
3’ reference supported (gene) 3271 64.89
5’ CAGE supported 65 1.29
3’ polyA supported 4077 80.88
Supported Novel Transcript Model (SNTM) 987 19.58
Non-canonical SJ incidence 1489 29.54
Full Illumina SJ support 1610 31.94
Intra-priming 26 0.52
RT-switching incidence 359 7.12

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 108
True Positive detections (TP) 63
SIRV transcripts associated to TP (Reference Match) 63
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 1
False Negative (FN) 21
False Positive (FP) 44
Sensitivity 0.75
Precision 0.58
Non Redundant Precision 0.58
Positive Detection Rate 0.75
False Discovery Rate 0.41
False Detection Rate 0.41
Redundancy 1.02