Your submission: ES_drna_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 9351
Number of known genes detected 9335
Number of transcripts detected 14598
Number of transcripts associated to a known gene 14521
Number of unique SJ detected 61318
Absolute value Relative value (%)
Novel SJ 125 0
Non-canonical SJ 115 0

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 11841 -
Reference Match 9955 84.07
5’ reference supported (transcript) 11075 93.53
3’ reference supported (transcript) 10168 85.87
5’ reference supported (gene) 11674 98.59
3’ reference supported (gene) 10830 91.46
5’ CAGE supported 201 1.7
3’ polyA supported 10148 85.7
Supported Reference Transcript Model (SRTM) 11558 97.61
Intra-priming 464 3.92
Reference redundancy Level 1.07 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2097 -
5’ reference supported (transcript) 24 1.14
3’ reference supported (transcript) 1110 52.93
5’ and 3’ reference supported (gene) 141 6.72
5’ reference supported (gene) 196 196
3’ reference supported (gene) 1485 70.82
5’ CAGE supported 2 0.1
3’ polyA supported 1994 95.09
Supported Reference Transcript Model (SRTM) 178 8.49
Intra-priming 15 0.72
Reference redundancy Level 1.01 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 583 -
5’ and 3’ reference supported (gene) 360 61.75
5’ reference supported (gene) 437 74.96
3’ reference supported (gene) 472 80.96
5’ CAGE supported 10 1.72
3’ polyA supported 551 94.51
Supported Novel Transcript Model (SNTM) 355 60.89
Intra-priming 7 1.2
Intron retention incidence 59 10.12

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 0 0
5’ and 3’ reference supported (gene) 0 0
5’ reference supported (gene) 0 0
3’ reference supported (gene) 0 0
5’ CAGE supported 0 0
3’ polyA supported 0 0
Supported Novel Transcript Model (SNTM) 0 0
Non-canonical SJ incidence 0 0
Full Illumina SJ support 0 0
Intra-priming 0 0
RT-switching incidence 0 0

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