Your submission: H1_mix_long_short 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 18584
Number of known genes detected 16676
Number of transcripts detected 46749
Number of transcripts associated to a known gene 44189
Number of unique SJ detected 146072
Absolute value Relative value (%)
Novel SJ 6891 0.05
Non-canonical SJ 1550 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 32728 -
Reference Match 23429 71.59
5’ reference supported (transcript) 26592 81.25
3’ reference supported (transcript) 26686 81.54
5’ reference supported (gene) 27943 85.38
3’ reference supported (gene) 28159 86.04
5’ CAGE supported 16175 49.42
3’ polyA supported 24997 76.38
Supported Reference Transcript Model (SRTM) 26580 81.21
Intra-priming 899 2.75
Reference redundancy Level 1.02 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1674 -
5’ reference supported (transcript) 399 23.84
3’ reference supported (transcript) 623 37.22
5’ and 3’ reference supported (gene) 487 29.09
5’ reference supported (gene) 765 765
3’ reference supported (gene) 1037 61.95
5’ CAGE supported 482 28.79
3’ polyA supported 1359 81.18
Supported Reference Transcript Model (SRTM) 706 42.17
Intra-priming 27 1.61
Reference redundancy Level 1.07 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 5535 -
5’ and 3’ reference supported (gene) 3823 69.07
5’ reference supported (gene) 4498 81.26
3’ reference supported (gene) 4626 83.58
5’ CAGE supported 3205 57.9
3’ polyA supported 5106 92.25
Supported Novel Transcript Model (SNTM) 3943 71.24
Intra-priming 59 1.07
Intron retention incidence 1155 20.87

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 4252 -
5’ and 3’ reference supported (gene) 1278 30.06
5’ reference supported (gene) 2861 67.29
3’ reference supported (gene) 2028 47.7
5’ CAGE supported 2182 51.32
3’ polyA supported 3217 75.66
Supported Novel Transcript Model (SNTM) 1591 37.42
Non-canonical SJ incidence 1417 33.33
Full Illumina SJ support 2648 62.28
Intra-priming 147 3.46
RT-switching incidence 406 9.55

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 92
True Positive detections (TP) 69
SIRV transcripts associated to TP (Reference Match) 69
Partial True Positive detections (PTP) 4
SIRV transcripts associated to PTP 5
False Negative (FN) 11
False Positive (FP) 17
Sensitivity 0.82
Precision 0.75
Non Redundant Precision 0.75
Positive Detection Rate 0.87
False Discovery Rate 0.23
False Detection Rate 0.18
Redundancy 1.03