Your submission: ES_CapTrap_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 13954
Number of known genes detected 13533
Number of transcripts detected 25816
Number of transcripts associated to a known gene 25376
Number of unique SJ detected 80757
Absolute value Relative value (%)
Novel SJ 970 0.01
Non-canonical SJ 56 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 24503 -
Reference Match 24503 100
5’ reference supported (transcript) 24503 100
3’ reference supported (transcript) 24503 100
5’ reference supported (gene) 24503 100
3’ reference supported (gene) 24503 100
5’ CAGE supported 381 1.55
3’ polyA supported 16462 67.18
Supported Reference Transcript Model (SRTM) 24503 100
Intra-priming 2091 8.53
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 468 -
5’ reference supported (transcript) 73 15.6
3’ reference supported (transcript) 226 48.29
5’ and 3’ reference supported (gene) 44 9.4
5’ reference supported (gene) 123 123
3’ reference supported (gene) 290 61.97
5’ CAGE supported 3 0.64
3’ polyA supported 424 90.6
Supported Reference Transcript Model (SRTM) 97 20.73
Intra-priming 10 2.14
Reference redundancy Level 1.01 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 99 -
5’ and 3’ reference supported (gene) 62 62.63
5’ reference supported (gene) 94 94.95
3’ reference supported (gene) 66 66.67
5’ CAGE supported 2 2.02
3’ polyA supported 84 84.85
Supported Novel Transcript Model (SNTM) 66 66.67
Intra-priming 1 1.01
Intron retention incidence 9 9.09

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 306 -
5’ and 3’ reference supported (gene) 115 37.58
5’ reference supported (gene) 186 60.78
3’ reference supported (gene) 171 55.88
5’ CAGE supported 5 1.63
3’ polyA supported 260 84.97
Supported Novel Transcript Model (SNTM) 41 13.4
Non-canonical SJ incidence 20 6.54
Full Illumina SJ support 136 44.44
Intra-priming 3 0.98
RT-switching incidence 23 7.52

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 71
True Positive detections (TP) 69
SIRV transcripts associated to TP (Reference Match) 69
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 15
False Positive (FP) 2
Sensitivity 0.82
Precision 0.97
Non Redundant Precision 0.97
Positive Detection Rate 0.82
False Discovery Rate 0.03
False Detection Rate 0.03
Redundancy 1