Your submission: WTC11_captrap_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 14290
Number of known genes detected 13980
Number of transcripts detected 38116
Number of transcripts associated to a known gene 37318
Number of unique SJ detected 115923
Absolute value Relative value (%)
Novel SJ 5042 0.04
Non-canonical SJ 394 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 29515 -
Reference Match 28927 98.01
5’ reference supported (transcript) 29150 98.76
3’ reference supported (transcript) 29188 98.89
5’ reference supported (gene) 29340 99.41
3’ reference supported (gene) 29314 99.32
5’ CAGE supported 21085 71.44
3’ polyA supported 24527 83.1
Supported Reference Transcript Model (SRTM) 29264 99.15
Intra-priming 857 2.9
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2270 -
5’ reference supported (transcript) 1053 46.39
3’ reference supported (transcript) 221 9.74
5’ and 3’ reference supported (gene) 417 18.37
5’ reference supported (gene) 1591 1591
3’ reference supported (gene) 719 31.67
5’ CAGE supported 1408 62.03
3’ polyA supported 1860 81.94
Supported Reference Transcript Model (SRTM) 1492 65.73
Intra-priming 237 10.44
Reference redundancy Level 1.19 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 2385 -
5’ and 3’ reference supported (gene) 1558 65.32
5’ reference supported (gene) 1874 78.57
3’ reference supported (gene) 1977 82.89
5’ CAGE supported 1509 63.27
3’ polyA supported 2319 97.23
Supported Novel Transcript Model (SNTM) 1710 71.7
Intra-priming 69 2.89
Intron retention incidence 229 9.6

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 3148 -
5’ and 3’ reference supported (gene) 692 21.98
5’ reference supported (gene) 1601 50.86
3’ reference supported (gene) 1503 47.74
5’ CAGE supported 1773 56.32
3’ polyA supported 3006 95.49
Supported Novel Transcript Model (SNTM) 1295 41.14
Non-canonical SJ incidence 237 7.53
Full Illumina SJ support 2034 64.61
Intra-priming 112 3.56
RT-switching incidence 147 4.67

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 78
True Positive detections (TP) 75
SIRV transcripts associated to TP (Reference Match) 75
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 9
False Positive (FP) 3
Sensitivity 0.89
Precision 0.96
Non Redundant Precision 0.96
Positive Detection Rate 0.89
False Discovery Rate 0.04
False Detection Rate 0.04
Redundancy 1