Your submission: H1_mix_cdna_ont_ls on ONT+Illumina 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 20329
Number of known genes detected 14456
Number of transcripts detected 52461
Number of transcripts associated to a known gene 45784
Number of unique SJ detected 105038
Absolute value Relative value (%)
Novel SJ 8383 0.08
Non-canonical SJ 344 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 30009 -
Reference Match 22690 75.61
5’ reference supported (transcript) 27641 92.11
3’ reference supported (transcript) 23447 78.13
5’ reference supported (gene) 28994 96.62
3’ reference supported (gene) 27004 89.99
5’ CAGE supported 20045 66.8
3’ polyA supported 26711 89.01
Supported Reference Transcript Model (SRTM) 29086 96.92
Intra-priming 529 1.76
Reference redundancy Level 1.1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2249 -
5’ reference supported (transcript) 372 16.54
3’ reference supported (transcript) 1015 45.13
5’ and 3’ reference supported (gene) 275 12.23
5’ reference supported (gene) 586 586
3’ reference supported (gene) 1325 58.92
5’ CAGE supported 550 24.46
3’ polyA supported 2087 92.8
Supported Reference Transcript Model (SRTM) 625 27.79
Intra-priming 31 1.38
Reference redundancy Level 1.11 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 10101 -
5’ and 3’ reference supported (gene) 7961 78.81
5’ reference supported (gene) 9345 92.52
3’ reference supported (gene) 8485 84
5’ CAGE supported 8230 81.48
3’ polyA supported 9967 98.67
Supported Novel Transcript Model (SNTM) 7321 72.48
Intra-priming 81 0.8
Intron retention incidence 1318 13.05

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 3425 -
5’ and 3’ reference supported (gene) 1794 52.38
5’ reference supported (gene) 2538 74.1
3’ reference supported (gene) 2389 69.75
5’ CAGE supported 2332 68.09
3’ polyA supported 3382 98.74
Supported Novel Transcript Model (SNTM) 2460 71.82
Non-canonical SJ incidence 145 4.23
Full Illumina SJ support 2990 87.3
Intra-priming 25 0.73
RT-switching incidence 183 5.34

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 108
True Positive detections (TP) 74
SIRV transcripts associated to TP (Reference Match) 74
Partial True Positive detections (PTP) 4
SIRV transcripts associated to PTP 6
False Negative (FN) 6
False Positive (FP) 28
Sensitivity 0.88
Precision 0.69
Non Redundant Precision 0.69
Positive Detection Rate 0.93
False Discovery Rate 0.3
False Detection Rate 0.26
Redundancy 1.03