Your submission: H1_mix_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 15072
Number of known genes detected 14732
Number of transcripts detected 40110
Number of transcripts associated to a known gene 39266
Number of unique SJ detected 124867
Absolute value Relative value (%)
Novel SJ 4859 0.04
Non-canonical SJ 409 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 31397 -
Reference Match 30838 98.22
5’ reference supported (transcript) 31051 98.9
3’ reference supported (transcript) 31077 98.98
5’ reference supported (gene) 31240 99.5
3’ reference supported (gene) 31197 99.36
5’ CAGE supported 20830 66.34
3’ polyA supported 25909 82.52
Supported Reference Transcript Model (SRTM) 31162 99.25
Intra-priming 1054 3.36
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2653 -
5’ reference supported (transcript) 1141 43.01
3’ reference supported (transcript) 272 10.25
5’ and 3’ reference supported (gene) 409 15.42
5’ reference supported (gene) 1766 1766
3’ reference supported (gene) 779 29.36
5’ CAGE supported 1017 38.33
3’ polyA supported 2058 77.57
Supported Reference Transcript Model (SRTM) 1441 54.32
Intra-priming 376 14.17
Reference redundancy Level 1.22 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 2340 -
5’ and 3’ reference supported (gene) 1437 61.41
5’ reference supported (gene) 1791 76.54
3’ reference supported (gene) 1855 79.27
5’ CAGE supported 943 40.3
3’ polyA supported 2246 95.98
Supported Novel Transcript Model (SNTM) 1523 65.09
Intra-priming 77 3.29
Intron retention incidence 263 11.24

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 2876 -
5’ and 3’ reference supported (gene) 588 20.45
5’ reference supported (gene) 1355 47.11
3’ reference supported (gene) 1410 49.03
5’ CAGE supported 804 27.96
3’ polyA supported 2711 94.26
Supported Novel Transcript Model (SNTM) 914 31.78
Non-canonical SJ incidence 225 7.82
Full Illumina SJ support 1913 66.52
Intra-priming 123 4.28
RT-switching incidence 148 5.15

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) 76
SIRV transcripts associated to TP (Reference Match) 76
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 8
False Positive (FP) 2
Sensitivity 0.9
Precision 0.97
Non Redundant Precision 0.97
Positive Detection Rate 0.9
False Discovery Rate 0.03
False Detection Rate 0.03
Redundancy 1