Your submission: H1_mix_cDNA_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 3947
Number of known genes detected 3275
Number of transcripts detected 7451
Number of transcripts associated to a known gene 6321
Number of unique SJ detected 19007
Absolute value Relative value (%)
Novel SJ 3964 0.21
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 2003 -
Reference Match 1040 51.92
5’ reference supported (transcript) 1554 77.58
3’ reference supported (transcript) 1335 66.65
5’ reference supported (gene) 1801 89.92
3’ reference supported (gene) 1698 84.77
5’ CAGE supported 1492 74.49
3’ polyA supported 1951 97.4
Supported Reference Transcript Model (SRTM) 1846 92.16
Intra-priming 3 0.15
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 425 -
5’ reference supported (transcript) 113 26.59
3’ reference supported (transcript) 210 49.41
5’ and 3’ reference supported (gene) 88 20.71
5’ reference supported (gene) 163 163
3’ reference supported (gene) 308 72.47
5’ CAGE supported 162 38.12
3’ polyA supported 390 91.76
Supported Reference Transcript Model (SRTM) 160 37.65
Intra-priming 0 0
Reference redundancy Level 1 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1106 -
5’ and 3’ reference supported (gene) 649 58.68
5’ reference supported (gene) 712 64.38
3’ reference supported (gene) 989 89.42
5’ CAGE supported 655 59.22
3’ polyA supported 1100 99.46
Supported Novel Transcript Model (SNTM) 585 52.89
Intra-priming 0 0
Intron retention incidence 135 12.21

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 2787 -
5’ and 3’ reference supported (gene) 2258 81.02
5’ reference supported (gene) 2521 90.46
3’ reference supported (gene) 2430 87.19
5’ CAGE supported 2344 84.1
3’ polyA supported 2738 98.24
Supported Novel Transcript Model (SNTM) 612 21.96
Non-canonical SJ incidence 0 0
Full Illumina SJ support 716 25.69
Intra-priming 0 0
RT-switching incidence 126 4.52

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 309
True Positive detections (TP) 19
SIRV transcripts associated to TP (Reference Match) 19
Partial True Positive detections (PTP) 3
SIRV transcripts associated to PTP 4
False Negative (FN) 62
False Positive (FP) 286
Sensitivity 0.23
Precision 0.06
Non Redundant Precision 0.06
Positive Detection Rate 0.26
False Discovery Rate 0.94
False Detection Rate 0.93
Redundancy 1.05