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 8266
Number of known genes detected 8207
Number of transcripts detected 24906
Number of transcripts associated to a known gene 24150
Number of unique SJ detected 68332
Absolute value Relative value (%)
Novel SJ 6432 0.09
Non-canonical SJ 8708 0.13

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 13971 -
Reference Match 8777 62.82
5’ reference supported (transcript) 11562 82.76
3’ reference supported (transcript) 9733 69.67
5’ reference supported (gene) 13295 95.16
3’ reference supported (gene) 11534 82.56
5’ CAGE supported 239 1.71
3’ polyA supported 12331 88.26
Supported Reference Transcript Model (SRTM) 12725 91.08
Intra-priming 471 3.37
Reference redundancy Level 1.27 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1895 -
5’ reference supported (transcript) 598 31.56
3’ reference supported (transcript) 701 36.99
5’ and 3’ reference supported (gene) 302 15.94
5’ reference supported (gene) 896 896
3’ reference supported (gene) 1053 55.57
5’ CAGE supported 22 1.16
3’ polyA supported 1510 79.68
Supported Reference Transcript Model (SRTM) 617 32.56
Intra-priming 128 6.75
Reference redundancy Level 1.17 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 2631 -
5’ and 3’ reference supported (gene) 1421 54.01
5’ reference supported (gene) 1764 67.05
3’ reference supported (gene) 1524 57.92
5’ CAGE supported 32 1.22
3’ polyA supported 1811 68.83
Supported Novel Transcript Model (SNTM) 1549 58.87
Intra-priming 31 1.18
Intron retention incidence 412 15.66

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 5653 -
5’ and 3’ reference supported (gene) 2828 50.03
5’ reference supported (gene) 3859 68.26
3’ reference supported (gene) 3584 63.4
5’ CAGE supported 67 1.19
3’ polyA supported 4594 81.27
Supported Novel Transcript Model (SNTM) 1152 20.38
Non-canonical SJ incidence 1306 23.1
Full Illumina SJ support 1972 34.88
Intra-priming 72 1.27
RT-switching incidence 270 4.78

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 100
True Positive detections (TP) 60
SIRV transcripts associated to TP (Reference Match) 60
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 2
False Negative (FN) 24
False Positive (FP) 38
Sensitivity 0.71
Precision 0.6
Non Redundant Precision 0.6
Positive Detection Rate 0.71
False Discovery Rate 0.38
False Detection Rate 0.38
Redundancy 1.03