Your submission: ES_CapTrap_PacBio on PacBio 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 9181
Number of known genes detected 8736
Number of transcripts detected 15038
Number of transcripts associated to a known gene 14461
Number of unique SJ detected 68704
Absolute value Relative value (%)
Novel SJ 2693 0.04
Non-canonical SJ 102 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 8892 -
Reference Match 3590 40.37
5’ reference supported (transcript) 6092 68.51
3’ reference supported (transcript) 5248 59.02
5’ reference supported (gene) 7838 88.15
3’ reference supported (gene) 6862 77.17
5’ CAGE supported 201 2.26
3’ polyA motif supported 201 2.26
Supported Reference Transcript Model (SRTM) 6099 68.59
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2792 -
5’ reference supported (transcript) 550 19.7
3’ reference supported (transcript) 1291 46.24
5’ and 3’ reference supported (gene) 331 11.86
5’ reference supported (gene) 872 872
3’ reference supported (gene) 1756 62.89
5’ CAGE supported 32 1.15
3’ polyA motif supported 32 1.15
Supported Reference Transcript Model (SRTM) 334 11.96
Reference redundancy Level 1.14 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1397 -
5’ and 3’ reference supported (gene) 995 71.22
5’ reference supported (gene) 1243 88.98
3’ reference supported (gene) 1106 79.17
5’ CAGE supported 27 1.93
3’ polyA motif supported 27 1.93
Supported Novel Transcript Model (SNTM) 908 65
Intron retention incidence 207 14.82

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 1380 -
5’ and 3’ reference supported (gene) 487 35.29
5’ reference supported (gene) 796 57.68
3’ reference supported (gene) 851 61.67
5’ CAGE supported 21 1.52
3’ polyA motif supported 21 1.52
Supported Novel Transcript Model (SNTM) 348 25.22
Non-canonical SJ incidence 106 7.68
Full Illumina SJ support 1029 74.57
RT-switching incidence 105 7.61

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 16
True Positive detections (TP) 15
SIRV transcripts associated to TP (Reference Match) 15
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 69
False Positive (FP) 1
Sensitivity 0.18
Precision 0.94
Non Redundant Precision 0.94
Positive Detection Rate 0.18
False Discovery Rate 0.06
False Detection Rate 0.06
Redundancy 1