Your submission: ES_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 18384
Number of known genes detected 13410
Number of transcripts detected 34605
Number of transcripts associated to a known gene 28884
Number of unique SJ detected 114074
Absolute value Relative value (%)
Novel SJ 7598 0.07
Non-canonical SJ 2098 0.02

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 19578 -
Reference Match 13028 66.54
5’ reference supported (transcript) 15217 77.72
3’ reference supported (transcript) 15216 77.72
5’ reference supported (gene) 16066 82.06
3’ reference supported (gene) 16049 81.97
5’ CAGE supported 277 1.41
3’ polyA supported 13571 69.32
Supported Reference Transcript Model (SRTM) 14715 75.16
Intra-priming 880 4.49
Reference redundancy Level 1.02 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1093 -
5’ reference supported (transcript) 248 22.69
3’ reference supported (transcript) 488 44.65
5’ and 3’ reference supported (gene) 256 23.42
5’ reference supported (gene) 453 453
3’ reference supported (gene) 699 63.95
5’ CAGE supported 6 0.55
3’ polyA supported 826 75.57
Supported Reference Transcript Model (SRTM) 355 32.48
Intra-priming 18 1.65
Reference redundancy Level 1.08 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 3458 -
5’ and 3’ reference supported (gene) 2353 68.05
5’ reference supported (gene) 2777 80.31
3’ reference supported (gene) 2888 83.52
5’ CAGE supported 67 1.94
3’ polyA supported 3131 90.54
Supported Novel Transcript Model (SNTM) 2395 69.26
Intra-priming 37 1.07
Intron retention incidence 504 14.57

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 4755 -
5’ and 3’ reference supported (gene) 1374 28.9
5’ reference supported (gene) 2962 62.29
3’ reference supported (gene) 2449 51.5
5’ CAGE supported 49 1.03
3’ polyA supported 3072 64.61
Supported Novel Transcript Model (SNTM) 1317 27.7
Non-canonical SJ incidence 1726 36.3
Full Illumina SJ support 2778 58.42
Intra-priming 321 6.75
RT-switching incidence 620 13.04

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 95
True Positive detections (TP) 69
SIRV transcripts associated to TP (Reference Match) 69
Partial True Positive detections (PTP) 6
SIRV transcripts associated to PTP 8
False Negative (FN) 9
False Positive (FP) 17
Sensitivity 0.82
Precision 0.73
Non Redundant Precision 0.73
Positive Detection Rate 0.89
False Discovery Rate 0.24
False Detection Rate 0.18
Redundancy 1.04