Your submission: H1_mix_drna_ont_ls on ONT+Illumina 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 9703
Number of known genes detected 9610
Number of transcripts detected 17746
Number of transcripts associated to a known gene 17561
Number of unique SJ detected 70684
Absolute value Relative value (%)
Novel SJ 827 0.01
Non-canonical SJ 153 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 15538 -
Reference Match 11802 75.96
5’ reference supported (transcript) 14544 93.6
3’ reference supported (transcript) 12149 78.19
5’ reference supported (gene) 15197 97.81
3’ reference supported (gene) 14058 90.47
5’ CAGE supported 11444 73.65
3’ polyA supported 14656 94.32
Supported Reference Transcript Model (SRTM) 15340 98.73
Intra-priming 199 1.28
Reference redundancy Level 1.08 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 540 -
5’ reference supported (transcript) 50 9.26
3’ reference supported (transcript) 289 53.52
5’ and 3’ reference supported (gene) 93 17.22
5’ reference supported (gene) 146 146
3’ reference supported (gene) 392 72.59
5’ CAGE supported 234 43.33
3’ polyA supported 512 94.81
Supported Reference Transcript Model (SRTM) 279 51.67
Intra-priming 3 0.56
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1108 -
5’ and 3’ reference supported (gene) 841 75.9
5’ reference supported (gene) 1000 90.25
3’ reference supported (gene) 916 82.67
5’ CAGE supported 828 74.73
3’ polyA supported 1095 98.83
Supported Novel Transcript Model (SNTM) 874 78.88
Intra-priming 5 0.45
Intron retention incidence 146 13.18

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 375 -
5’ and 3’ reference supported (gene) 195 52
5’ reference supported (gene) 291 77.6
3’ reference supported (gene) 266 70.93
5’ CAGE supported 280 74.67
3’ polyA supported 372 99.2
Supported Novel Transcript Model (SNTM) 296 78.93
Non-canonical SJ incidence 60 16
Full Illumina SJ support 307 81.87
Intra-priming 5 1.33
RT-switching incidence 61 16.27

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