Your submission: WTC11_FreeStyle on PacBio+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 20658
Number of known genes detected 15194
Number of transcripts detected 67410
Number of transcripts associated to a known gene 60782
Number of unique SJ detected 150499
Absolute value Relative value (%)
Novel SJ 7181 0.05
Non-canonical SJ 544 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 36423 -
Reference Match 14381 39.48
5’ reference supported (transcript) 25980 71.33
3’ reference supported (transcript) 20128 55.26
5’ reference supported (gene) 31787 87.27
3’ reference supported (gene) 28539 78.35
5’ CAGE supported 31698 87.03
3’ polyA supported 35123 96.43
Supported Reference Transcript Model (SRTM) 33752 92.67
Intra-priming 1724 4.73
Reference redundancy Level 1.55 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 4406 -
5’ reference supported (transcript) 1939 44.01
3’ reference supported (transcript) 1655 37.56
5’ and 3’ reference supported (gene) 1312 29.78
5’ reference supported (gene) 2753 2753
3’ reference supported (gene) 2616 59.37
5’ CAGE supported 3037 68.93
3’ polyA supported 3636 82.52
Supported Reference Transcript Model (SRTM) 2694 61.14
Intra-priming 836 18.97
Reference redundancy Level 1.33 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 15874 -
5’ and 3’ reference supported (gene) 12029 75.78
5’ reference supported (gene) 14464 91.12
3’ reference supported (gene) 13102 82.54
5’ CAGE supported 14127 88.99
3’ polyA supported 14943 94.14
Supported Novel Transcript Model (SNTM) 12912 81.34
Intra-priming 1270 8
Intron retention incidence 4053 25.53

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 4079 -
5’ and 3’ reference supported (gene) 1996 48.93
5’ reference supported (gene) 2894 70.95
3’ reference supported (gene) 2818 69.09
5’ CAGE supported 3391 83.13
3’ polyA supported 3937 96.52
Supported Novel Transcript Model (SNTM) 2941 72.1
Non-canonical SJ incidence 490 12.01
Full Illumina SJ support 3352 82.18
Intra-priming 221 5.42
RT-switching incidence 276 6.77

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 85
True Positive detections (TP) 82
SIRV transcripts associated to TP (Reference Match) 82
Partial True Positive detections (PTP) 1
SIRV transcripts associated to PTP 2
False Negative (FN) 1
False Positive (FP) 1
Sensitivity 0.98
Precision 0.96
Non Redundant Precision 0.96
Positive Detection Rate 0.99
False Discovery Rate 0.02
False Detection Rate 0.01
Redundancy 1.01