Your submission: H1_mix_CapTrap_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 4917
Number of known genes detected 4560
Number of transcripts detected 8358
Number of transcripts associated to a known gene 7479
Number of unique SJ detected 18937
Absolute value Relative value (%)
Novel SJ 3534 0.19
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 1922 -
Reference Match 859 44.69
5’ reference supported (transcript) 1374 71.49
3’ reference supported (transcript) 1208 62.85
5’ reference supported (gene) 1632 84.91
3’ reference supported (gene) 1640 85.33
5’ CAGE supported 1358 70.66
3’ polyA supported 1891 98.39
Supported Reference Transcript Model (SRTM) 1666 86.68
Intra-priming 6 0.31
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1644 -
5’ reference supported (transcript) 193 11.74
3’ reference supported (transcript) 896 54.5
5’ and 3’ reference supported (gene) 123 7.48
5’ reference supported (gene) 279 279
3’ reference supported (gene) 1216 73.97
5’ CAGE supported 251 15.27
3’ polyA supported 1583 96.29
Supported Reference Transcript Model (SRTM) 274 16.67
Intra-priming 6 0.36
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1301 -
5’ and 3’ reference supported (gene) 736 56.57
5’ reference supported (gene) 821 63.11
3’ reference supported (gene) 1131 86.93
5’ CAGE supported 760 58.42
3’ polyA supported 1292 99.31
Supported Novel Transcript Model (SNTM) 723 55.57
Intra-priming 0 0
Intron retention incidence 144 11.07

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 2612 -
5’ and 3’ reference supported (gene) 1935 74.08
5’ reference supported (gene) 2224 85.15
3’ reference supported (gene) 2215 84.8
5’ CAGE supported 2130 81.55
3’ polyA supported 2584 98.93
Supported Novel Transcript Model (SNTM) 674 25.8
Non-canonical SJ incidence 0 0
Full Illumina SJ support 833 31.89
Intra-priming 1 0.04
RT-switching incidence 100 3.83

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 208
True Positive detections (TP) 13
SIRV transcripts associated to TP (Reference Match) 13
Partial True Positive detections (PTP) 8
SIRV transcripts associated to PTP 8
False Negative (FN) 63
False Positive (FP) 187
Sensitivity 0.15
Precision 0.06
Non Redundant Precision 0.06
Positive Detection Rate 0.25
False Discovery Rate 0.94
False Detection Rate 0.9
Redundancy 1