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 13888
Number of known genes detected 13375
Number of transcripts detected 23720
Number of transcripts associated to a known gene 23169
Number of unique SJ detected 83836
Absolute value Relative value (%)
Novel SJ 1096 0.01
Non-canonical SJ 254 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 22679 -
Reference Match 22678 100
5’ reference supported (transcript) 22678 100
3’ reference supported (transcript) 22679 100
5’ reference supported (gene) 22678 100
3’ reference supported (gene) 22679 100
5’ CAGE supported 248 1.09
3’ polyA supported 15390 67.86
Supported Reference Transcript Model (SRTM) 22678 100
Intra-priming 1913 8.44
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 145 -
5’ reference supported (transcript) 26 17.93
3’ reference supported (transcript) 83 57.24
5’ and 3’ reference supported (gene) 22 15.17
5’ reference supported (gene) 51 51
3’ reference supported (gene) 97 66.9
5’ CAGE supported 2 1.38
3’ polyA supported 125 86.21
Supported Reference Transcript Model (SRTM) 34 23.45
Intra-priming 1 0.69
Reference redundancy Level 1.01 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 59 -
5’ and 3’ reference supported (gene) 37 62.71
5’ reference supported (gene) 52 88.14
3’ reference supported (gene) 44 74.58
5’ CAGE supported 2 3.39
3’ polyA supported 53 89.83
Supported Novel Transcript Model (SNTM) 37 62.71
Intra-priming 0 0
Intron retention incidence 6 10.17

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 286 -
5’ and 3’ reference supported (gene) 146 51.05
5’ reference supported (gene) 197 68.88
3’ reference supported (gene) 192 67.13
5’ CAGE supported 6 2.1
3’ polyA supported 254 88.81
Supported Novel Transcript Model (SNTM) 23 8.04
Non-canonical SJ incidence 94 32.87
Full Illumina SJ support 82 28.67
Intra-priming 4 1.4
RT-switching incidence 21 7.34

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 73
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) 4
Sensitivity 0.82
Precision 0.95
Non Redundant Precision 0.95
Positive Detection Rate 0.82
False Discovery Rate 0.05
False Detection Rate 0.05
Redundancy 1