Your submission: H1_mix_R2C2_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 4219
Number of known genes detected 4172
Number of transcripts detected 4734
Number of transcripts associated to a known gene 4685
Number of unique SJ detected 2644
Absolute value Relative value (%)
Novel SJ 62 0.02
Non-canonical SJ 23 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 4562 -
Reference Match 4521 99.1
5’ reference supported (transcript) 4536 99.43
3’ reference supported (transcript) 4534 99.39
5’ reference supported (gene) 4544 99.61
3’ reference supported (gene) 4537 99.45
5’ CAGE supported 1117 24.48
3’ polyA supported 2676 58.66
Supported Reference Transcript Model (SRTM) 4539 99.5
Intra-priming 219 4.8
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 107 -
5’ reference supported (transcript) 16 14.95
3’ reference supported (transcript) 33 30.84
5’ and 3’ reference supported (gene) 4 3.74
5’ reference supported (gene) 22 22
3’ reference supported (gene) 49 45.79
5’ CAGE supported 19 17.76
3’ polyA supported 69 64.49
Supported Reference Transcript Model (SRTM) 10 9.35
Intra-priming 3 2.8
Reference redundancy Level 1.01 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 5 -
5’ and 3’ reference supported (gene) 0 0
5’ reference supported (gene) 0 0
3’ reference supported (gene) 3 60
5’ CAGE supported 0 0
3’ polyA supported 3 60
Supported Novel Transcript Model (SNTM) 0 0
Intra-priming 0 0
Intron retention incidence 1 20

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 11 -
5’ and 3’ reference supported (gene) 0 0
5’ reference supported (gene) 1 9.09
3’ reference supported (gene) 3 27.27
5’ CAGE supported 0 0
3’ polyA supported 7 63.64
Supported Novel Transcript Model (SNTM) 0 0
Non-canonical SJ incidence 4 36.36
Full Illumina SJ support 4 36.36
Intra-priming 0 0
RT-switching incidence 2 18.18

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 28
True Positive detections (TP) 28
SIRV transcripts associated to TP (Reference Match) 28
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 56
False Positive (FP) 0
Sensitivity 0.33
Precision 1
Non Redundant Precision 1
Positive Detection Rate 0.33
False Discovery Rate 0
False Detection Rate 0
Redundancy 1