Your submission: H1_mix_FreeStyle on PacBio+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 21059
Number of known genes detected 15213
Number of transcripts detected 67916
Number of transcripts associated to a known gene 60752
Number of unique SJ detected 150175
Absolute value Relative value (%)
Novel SJ 6685 0.04
Non-canonical SJ 593 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 36287 -
Reference Match 14311 39.44
5’ reference supported (transcript) 25783 71.05
3’ reference supported (transcript) 20101 55.39
5’ reference supported (gene) 31588 87.05
3’ reference supported (gene) 28564 78.72
5’ CAGE supported 30058 82.83
3’ polyA supported 35100 96.73
Supported Reference Transcript Model (SRTM) 32908 90.69
Intra-priming 1709 4.71
Reference redundancy Level 1.54 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 4364 -
5’ reference supported (transcript) 1985 45.49
3’ reference supported (transcript) 1636 37.49
5’ and 3’ reference supported (gene) 1366 31.3
5’ reference supported (gene) 2827 2827
3’ reference supported (gene) 2586 59.26
5’ CAGE supported 2767 63.41
3’ polyA supported 3513 80.5
Supported Reference Transcript Model (SRTM) 2452 56.19
Intra-priming 1036 23.74
Reference redundancy Level 1.32 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 16217 -
5’ and 3’ reference supported (gene) 12192 75.18
5’ reference supported (gene) 14758 91
3’ reference supported (gene) 13280 81.89
5’ CAGE supported 13925 85.87
3’ polyA supported 15047 92.79
Supported Novel Transcript Model (SNTM) 12913 79.63
Intra-priming 1517 9.35
Intron retention incidence 4393 27.09

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 3884 -
5’ and 3’ reference supported (gene) 1870 48.15
5’ reference supported (gene) 2632 67.77
3’ reference supported (gene) 2728 70.24
5’ CAGE supported 2741 70.57
3’ polyA supported 3707 95.44
Supported Novel Transcript Model (SNTM) 2387 61.46
Non-canonical SJ incidence 564 14.52
Full Illumina SJ support 3107 79.99
Intra-priming 237 6.1
RT-switching incidence 279 7.18

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 84
True Positive detections (TP) 82
SIRV transcripts associated to TP (Reference Match) 82
Partial True Positive detections (PTP) 1
SIRV transcripts associated to PTP 1
False Negative (FN) 1
False Positive (FP) 1
Sensitivity 0.98
Precision 0.98
Non Redundant Precision 0.98
Positive Detection Rate 0.99
False Discovery Rate 0.02
False Detection Rate 0.01
Redundancy 1