Your submission: iso_detect_ref_spectra_H1_mix on PacBio 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 30646
Number of known genes detected 21395
Number of transcripts detected 169203
Number of transcripts associated to a known gene 153713
Number of unique SJ detected 280087
Absolute value Relative value (%)
Novel SJ 77556 0.28
Non-canonical SJ 21085 0.08

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 46525 -
Reference Match 14353 30.85
5’ reference supported (transcript) 27004 58.04
3’ reference supported (transcript) 23700 50.94
5’ reference supported (gene) 34953 75.13
3’ reference supported (gene) 37557 80.72
5’ CAGE supported 29873 64.21
3’ polyA supported 44697 96.07
Supported Reference Transcript Model (SRTM) 35623 76.57
Intra-priming 3612 7.76
Reference redundancy Level 1.06 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 17610 -
5’ reference supported (transcript) 2964 16.83
3’ reference supported (transcript) 8972 50.95
5’ and 3’ reference supported (gene) 2806 15.93
5’ reference supported (gene) 5019 5019
3’ reference supported (gene) 12636 71.75
5’ CAGE supported 4093 23.24
3’ polyA supported 17181 97.56
Supported Reference Transcript Model (SRTM) 5478 31.11
Intra-priming 719 4.08
Reference redundancy Level 1.51 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 42391 -
5’ and 3’ reference supported (gene) 30077 70.95
5’ reference supported (gene) 35687 84.19
3’ reference supported (gene) 35280 83.23
5’ CAGE supported 31788 74.99
3’ polyA supported 41758 98.51
Supported Novel Transcript Model (SNTM) 29051 68.53
Intra-priming 1499 3.54
Intron retention incidence 18817 44.39

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 47187 -
5’ and 3’ reference supported (gene) 25966 55.03
5’ reference supported (gene) 34955 74.08
3’ reference supported (gene) 33668 71.35
5’ CAGE supported 32129 68.09
3’ polyA supported 46150 97.8
Supported Novel Transcript Model (SNTM) 14323 30.35
Non-canonical SJ incidence 10314 21.86
Full Illumina SJ support 17892 37.92
Intra-priming 1954 4.14
RT-switching incidence 2807 5.95

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 269
True Positive detections (TP) 80
SIRV transcripts associated to TP (Reference Match) 80
Partial True Positive detections (PTP) 1
SIRV transcripts associated to PTP 44
False Negative (FN) 3
False Positive (FP) 145
Sensitivity 0.95
Precision 0.3
Non Redundant Precision 0.3
Positive Detection Rate 0.96
False Discovery Rate 0.54
False Detection Rate 0.54
Redundancy 1.53