Your submission: ES_R2C2only 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 14140
Number of known genes detected 11698
Number of transcripts detected 36177
Number of transcripts associated to a known gene 33339
Number of unique SJ detected 108200
Absolute value Relative value (%)
Novel SJ 3639 0.03
Non-canonical SJ 578 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 21585 -
Reference Match 8124 37.64
5’ reference supported (transcript) 14036 65.03
3’ reference supported (transcript) 12392 57.41
5’ reference supported (gene) 18239 84.5
3’ reference supported (gene) 16281 75.43
5’ CAGE supported 503 2.33
3’ polyA supported 19556 90.6
Supported Reference Transcript Model (SRTM) 17187 79.62
Intra-priming 2028 9.4
Reference redundancy Level 1.49 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2831 -
5’ reference supported (transcript) 1156 40.83
3’ reference supported (transcript) 1034 36.52
5’ and 3’ reference supported (gene) 701 24.76
5’ reference supported (gene) 1669 1669
3’ reference supported (gene) 1539 54.36
5’ CAGE supported 44 1.55
3’ polyA supported 1989 70.26
Supported Reference Transcript Model (SRTM) 1118 39.49
Intra-priming 742 26.21
Reference redundancy Level 1.25 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 6348 -
5’ and 3’ reference supported (gene) 4428 69.75
5’ reference supported (gene) 5667 89.27
3’ reference supported (gene) 4936 77.76
5’ CAGE supported 103 1.62
3’ polyA supported 5388 84.88
Supported Novel Transcript Model (SNTM) 4480 70.57
Intra-priming 1055 16.62
Intron retention incidence 1408 22.18

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 2575 -
5’ and 3’ reference supported (gene) 1120 43.5
5’ reference supported (gene) 1569 60.93
3’ reference supported (gene) 1858 72.16
5’ CAGE supported 27 1.05
3’ polyA supported 2271 88.19
Supported Novel Transcript Model (SNTM) 916 35.57
Non-canonical SJ incidence 538 20.89
Full Illumina SJ support 1815 70.49
Intra-priming 250 9.71
RT-switching incidence 259 10.06

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 98
True Positive detections (TP) 68
SIRV transcripts associated to TP (Reference Match) 68
Partial True Positive detections (PTP) 10
SIRV transcripts associated to PTP 30
False Negative (FN) 6
False Positive (FP) 0
Sensitivity 0.81
Precision 0.69
Non Redundant Precision 0.69
Positive Detection Rate 0.93
False Discovery Rate 0.1
False Detection Rate 0
Redundancy 1.26