Your submission: H1_mix_r2c2_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 13940
Number of known genes detected 13896
Number of transcripts detected 38502
Number of transcripts associated to a known gene 38345
Number of unique SJ detected 139798
Absolute value Relative value (%)
Novel SJ 2284 0.02
Non-canonical SJ 396 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 30225 -
Reference Match 29818 98.65
5’ reference supported (transcript) 29973 99.17
3’ reference supported (transcript) 29988 99.22
5’ reference supported (gene) 30111 99.62
3’ reference supported (gene) 30083 99.53
5’ CAGE supported 22207 73.47
3’ polyA supported 25194 83.35
Supported Reference Transcript Model (SRTM) 30064 99.47
Intra-priming 878 2.9
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2764 -
5’ reference supported (transcript) 1300 47.03
3’ reference supported (transcript) 173 6.26
5’ and 3’ reference supported (gene) 540 19.54
5’ reference supported (gene) 1921 1921
3’ reference supported (gene) 768 27.79
5’ CAGE supported 1132 40.96
3’ polyA supported 2214 80.1
Supported Reference Transcript Model (SRTM) 1645 59.52
Intra-priming 287 10.38
Reference redundancy Level 1.39 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 3849 -
5’ and 3’ reference supported (gene) 2503 65.03
5’ reference supported (gene) 2979 77.4
3’ reference supported (gene) 3211 83.42
5’ CAGE supported 1709 44.4
3’ polyA supported 3719 96.62
Supported Novel Transcript Model (SNTM) 2769 71.94
Intra-priming 132 3.43
Intron retention incidence 988 25.67

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 1507 -
5’ and 3’ reference supported (gene) 644 42.73
5’ reference supported (gene) 914 60.65
3’ reference supported (gene) 1033 68.55
5’ CAGE supported 586 38.89
3’ polyA supported 1428 94.76
Supported Novel Transcript Model (SNTM) 631 41.87
Non-canonical SJ incidence 272 18.05
Full Illumina SJ support 1048 69.54
Intra-priming 61 4.05
RT-switching incidence 149 9.89

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 80
True Positive detections (TP) 77
SIRV transcripts associated to TP (Reference Match) 77
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 2
False Negative (FN) 7
False Positive (FP) 1
Sensitivity 0.92
Precision 0.96
Non Redundant Precision 0.96
Positive Detection Rate 0.92
False Discovery Rate 0.01
False Detection Rate 0.01
Redundancy 1.03