Your submission: WTC11_CapTrap_PacBio 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 2941
Number of known genes detected 2866
Number of transcripts detected 4171
Number of transcripts associated to a known gene 3992
Number of unique SJ detected 14906
Absolute value Relative value (%)
Novel SJ 668 0.04
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 2069 -
Reference Match 1085 52.44
5’ reference supported (transcript) 1652 79.85
3’ reference supported (transcript) 1364 65.93
5’ reference supported (gene) 1916 92.61
3’ reference supported (gene) 1830 88.45
5’ CAGE supported 1776 85.84
3’ polyA supported 2046 98.89
Supported Reference Transcript Model (SRTM) 1970 95.22
Intra-priming 3 0.14
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 868 -
5’ reference supported (transcript) 90 10.37
3’ reference supported (transcript) 512 58.99
5’ and 3’ reference supported (gene) 92 10.6
5’ reference supported (gene) 148 148
3’ reference supported (gene) 709 81.68
5’ CAGE supported 189 21.77
3’ polyA supported 847 97.58
Supported Reference Transcript Model (SRTM) 205 23.62
Intra-priming 2 0.23
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 676 -
5’ and 3’ reference supported (gene) 516 76.33
5’ reference supported (gene) 549 81.21
3’ reference supported (gene) 621 91.86
5’ CAGE supported 530 78.4
3’ polyA supported 671 99.26
Supported Novel Transcript Model (SNTM) 525 77.66
Intra-priming 0 0
Intron retention incidence 90 13.31

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 379 -
5’ and 3’ reference supported (gene) 258 68.07
5’ reference supported (gene) 315 83.11
3’ reference supported (gene) 313 82.59
5’ CAGE supported 339 89.45
3’ polyA supported 379 100
Supported Novel Transcript Model (SNTM) 296 78.1
Non-canonical SJ incidence 0 0
Full Illumina SJ support 311 82.06
Intra-priming 0 0
RT-switching incidence 21 5.54

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 73
True Positive detections (TP) 47
SIRV transcripts associated to TP (Reference Match) 47
Partial True Positive detections (PTP) 6
SIRV transcripts associated to PTP 6
False Negative (FN) 31
False Positive (FP) 20
Sensitivity 0.56
Precision 0.64
Non Redundant Precision 0.64
Positive Detection Rate 0.63
False Discovery Rate 0.36
False Detection Rate 0.27
Redundancy 1