Your submission: H1_mix_drna_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 9759
Number of known genes detected 9736
Number of transcripts detected 17531
Number of transcripts associated to a known gene 17455
Number of unique SJ detected 68679
Absolute value Relative value (%)
Novel SJ 327 0
Non-canonical SJ 153 0

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 14001 -
Reference Match 11730 83.78
5’ reference supported (transcript) 13311 95.07
3’ reference supported (transcript) 11999 85.7
5’ reference supported (gene) 13728 98.05
3’ reference supported (gene) 13094 93.52
5’ CAGE supported 9785 69.89
3’ polyA supported 13120 93.71
Supported Reference Transcript Model (SRTM) 13688 97.76
Intra-priming 196 1.4
Reference redundancy Level 1.05 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2530 -
5’ reference supported (transcript) 32 1.26
3’ reference supported (transcript) 1257 49.68
5’ and 3’ reference supported (gene) 294 11.62
5’ reference supported (gene) 367 367
3’ reference supported (gene) 1877 74.19
5’ CAGE supported 115 4.55
3’ polyA supported 2442 96.52
Supported Reference Transcript Model (SRTM) 402 15.89
Intra-priming 19 0.75
Reference redundancy Level 1.01 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 863 -
5’ and 3’ reference supported (gene) 538 62.34
5’ reference supported (gene) 623 72.19
3’ reference supported (gene) 706 81.81
5’ CAGE supported 432 50.06
3’ polyA supported 849 98.38
Supported Novel Transcript Model (SNTM) 528 61.18
Intra-priming 4 0.46
Intron retention incidence 106 12.28

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 61 -
5’ and 3’ reference supported (gene) 27 44.26
5’ reference supported (gene) 35 57.38
3’ reference supported (gene) 49 80.33
5’ CAGE supported 26 42.62
3’ polyA supported 60 98.36
Supported Novel Transcript Model (SNTM) 0 0
Non-canonical SJ incidence 59 96.72
Full Illumina SJ support 0 0
Intra-priming 3 4.92
RT-switching incidence 44 72.13

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 77
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) 2
Sensitivity 0.89
Precision 0.97
Non Redundant Precision 0.97
Positive Detection Rate 0.89
False Discovery Rate 0.03
False Detection Rate 0.03
Redundancy 1