Your submission: ES_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 13385
Number of known genes detected 13079
Number of transcripts detected 27866
Number of transcripts associated to a known gene 27079
Number of unique SJ detected 106638
Absolute value Relative value (%)
Novel SJ 4323 0.04
Non-canonical SJ 588 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 21422 -
Reference Match 21421 100
5’ reference supported (transcript) 21421 100
3’ reference supported (transcript) 21422 100
5’ reference supported (gene) 21421 100
3’ reference supported (gene) 21422 100
5’ CAGE supported 341 1.59
3’ polyA supported 16365 76.39
Supported Reference Transcript Model (SRTM) 21421 100
Intra-priming 1495 6.98
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1560 -
5’ reference supported (transcript) 608 38.97
3’ reference supported (transcript) 260 16.67
5’ and 3’ reference supported (gene) 195 12.5
5’ reference supported (gene) 901 901
3’ reference supported (gene) 510 32.69
5’ CAGE supported 7 0.45
3’ polyA supported 1105 70.83
Supported Reference Transcript Model (SRTM) 632 40.51
Intra-priming 159 10.19
Reference redundancy Level 1.19 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1497 -
5’ and 3’ reference supported (gene) 862 57.58
5’ reference supported (gene) 1069 71.41
3’ reference supported (gene) 1188 79.36
5’ CAGE supported 18 1.2
3’ polyA supported 1340 89.51
Supported Novel Transcript Model (SNTM) 930 62.12
Intra-priming 45 3.01
Intron retention incidence 144 9.62

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 2600 -
5’ and 3’ reference supported (gene) 453 17.42
5’ reference supported (gene) 976 37.54
3’ reference supported (gene) 1344 51.69
5’ CAGE supported 22 0.85
3’ polyA supported 2007 77.19
Supported Novel Transcript Model (SNTM) 518 19.92
Non-canonical SJ incidence 250 9.62
Full Illumina SJ support 1730 66.54
Intra-priming 60 2.31
RT-switching incidence 157 6.04

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 75
True Positive detections (TP) 73
SIRV transcripts associated to TP (Reference Match) 73
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 11
False Positive (FP) 2
Sensitivity 0.87
Precision 0.97
Non Redundant Precision 0.97
Positive Detection Rate 0.87
False Discovery Rate 0.03
False Detection Rate 0.03
Redundancy 1