Your submission: ES_drna_ont_ls on ONT+Illumina 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 9433
Number of known genes detected 9387
Number of transcripts detected 14932
Number of transcripts associated to a known gene 14792
Number of unique SJ detected 61760
Absolute value Relative value (%)
Novel SJ 410 0.01
Non-canonical SJ 115 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 11891 -
Reference Match 9952 83.69
5’ reference supported (transcript) 11072 93.11
3’ reference supported (transcript) 10185 85.65
5’ reference supported (gene) 11690 98.31
3’ reference supported (gene) 10860 91.33
5’ CAGE supported 261 2.19
3’ polyA supported 10194 85.73
Supported Reference Transcript Model (SRTM) 11610 97.64
Intra-priming 459 3.86
Reference redundancy Level 1.07 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2085 -
5’ reference supported (transcript) 25 1.2
3’ reference supported (transcript) 1116 53.53
5’ and 3’ reference supported (gene) 131 6.28
5’ reference supported (gene) 181 181
3’ reference supported (gene) 1480 70.98
5’ CAGE supported 55 2.64
3’ polyA supported 1981 95.01
Supported Reference Transcript Model (SRTM) 217 10.41
Intra-priming 15 0.72
Reference redundancy Level 1.01 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 597 -
5’ and 3’ reference supported (gene) 368 61.64
5’ reference supported (gene) 445 74.54
3’ reference supported (gene) 484 81.07
5’ CAGE supported 18 3.02
3’ polyA supported 565 94.64
Supported Novel Transcript Model (SNTM) 368 61.64
Intra-priming 8 1.34
Intron retention incidence 60 10.05

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 219 -
5’ and 3’ reference supported (gene) 130 59.36
5’ reference supported (gene) 184 84.02
3’ reference supported (gene) 158 72.15
5’ CAGE supported 5 2.28
3’ polyA supported 207 94.52
Supported Novel Transcript Model (SNTM) 157 71.69
Non-canonical SJ incidence 1 0.46
Full Illumina SJ support 208 94.98
Intra-priming 3 1.37
RT-switching incidence 13 5.94

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 78
True Positive detections (TP) 76
SIRV transcripts associated to TP (Reference Match) 76
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 8
False Positive (FP) 2
Sensitivity 0.9
Precision 0.97
Non Redundant Precision 0.97
Positive Detection Rate 0.9
False Discovery Rate 0.03
False Detection Rate 0.03
Redundancy 1