Your submission: H1_mix_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 7131
Number of known genes detected 7131
Number of transcripts detected 15187
Number of transcripts associated to a known gene 15179
Number of unique SJ detected 66370
Absolute value Relative value (%)
Novel SJ 876 0.01
Non-canonical SJ 266 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 13373 -
Reference Match 8662 64.77
5’ reference supported (transcript) 11909 89.05
3’ reference supported (transcript) 9385 70.18
5’ reference supported (gene) 13081 97.82
3’ reference supported (gene) 11808 88.3
5’ CAGE supported 10507 78.57
3’ polyA supported 13188 98.62
Supported Reference Transcript Model (SRTM) 13126 98.15
Intra-priming 77 0.58
Reference redundancy Level 1.21 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 497 -
5’ reference supported (transcript) 70 14.08
3’ reference supported (transcript) 278 55.94
5’ and 3’ reference supported (gene) 130 26.16
5’ reference supported (gene) 187 187
3’ reference supported (gene) 395 79.48
5’ CAGE supported 144 28.97
3’ polyA supported 475 95.57
Supported Reference Transcript Model (SRTM) 197 39.64
Intra-priming 2 0.4
Reference redundancy Level 1.15 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 539 -
5’ and 3’ reference supported (gene) 475 88.13
5’ reference supported (gene) 512 94.99
3’ reference supported (gene) 501 92.95
5’ CAGE supported 387 71.8
3’ polyA supported 537 99.63
Supported Novel Transcript Model (SNTM) 463 85.9
Intra-priming 1 0.19
Intron retention incidence 78 14.47

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 770 -
5’ and 3’ reference supported (gene) 568 73.77
5’ reference supported (gene) 647 84.03
3’ reference supported (gene) 673 87.4
5’ CAGE supported 492 63.9
3’ polyA supported 765 99.35
Supported Novel Transcript Model (SNTM) 162 21.04
Non-canonical SJ incidence 197 25.58
Full Illumina SJ support 187 24.29
Intra-priming 0 0
RT-switching incidence 82 10.65

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 76
True Positive detections (TP) 67
SIRV transcripts associated to TP (Reference Match) 67
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 1
False Negative (FN) 17
False Positive (FP) 8
Sensitivity 0.8
Precision 0.88
Non Redundant Precision 0.88
Positive Detection Rate 0.8
False Discovery Rate 0.11
False Detection Rate 0.11
Redundancy 1.01