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 10285
Number of known genes detected 10016
Number of transcripts detected 21899
Number of transcripts associated to a known gene 21493
Number of unique SJ detected 92052
Absolute value Relative value (%)
Novel SJ 3193 0.03
Non-canonical SJ 105 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 10466 -
Reference Match 4252 40.63
5’ reference supported (transcript) 6627 63.32
3’ reference supported (transcript) 6564 62.72
5’ reference supported (gene) 8663 82.77
3’ reference supported (gene) 8457 80.8
5’ CAGE supported 210 2.01
3’ polyA motif supported 210 2.01
Supported Reference Transcript Model (SRTM) 7050 67.36
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 7013 -
5’ reference supported (transcript) 268 3.82
3’ reference supported (transcript) 4238 60.43
5’ and 3’ reference supported (gene) 499 7.12
5’ reference supported (gene) 773 773
3’ reference supported (gene) 5367 76.53
5’ CAGE supported 20 0.29
3’ polyA motif supported 20 0.29
Supported Reference Transcript Model (SRTM) 507 7.23
Reference redundancy Level 1.36 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1540 -
5’ and 3’ reference supported (gene) 931 60.45
5’ reference supported (gene) 1129 73.31
3’ reference supported (gene) 1272 82.6
5’ CAGE supported 23 1.49
3’ polyA motif supported 23 1.49
Supported Novel Transcript Model (SNTM) 874 56.75
Intron retention incidence 350 22.73

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 2474 -
5’ and 3’ reference supported (gene) 1198 48.42
5’ reference supported (gene) 1594 64.43
3’ reference supported (gene) 1812 73.24
5’ CAGE supported 47 1.9
3’ polyA motif supported 47 1.9
Supported Novel Transcript Model (SNTM) 333 13.46
Non-canonical SJ incidence 111 4.49
Full Illumina SJ support 876 35.41
RT-switching incidence 239 9.66

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 14
True Positive detections (TP) 12
SIRV transcripts associated to TP (Reference Match) 12
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 72
False Positive (FP) 2
Sensitivity 0.14
Precision 0.86
Non Redundant Precision 0.86
Positive Detection Rate 0.14
False Discovery Rate 0.14
False Detection Rate 0.14
Redundancy 1