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 11145
Number of known genes detected 10746
Number of transcripts detected 19435
Number of transcripts associated to a known gene 18985
Number of unique SJ detected 81330
Absolute value Relative value (%)
Novel SJ 1256 0.02
Non-canonical SJ 67 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 17457 -
Reference Match 17457 100
5’ reference supported (transcript) 17457 100
3’ reference supported (transcript) 17457 100
5’ reference supported (gene) 17457 100
3’ reference supported (gene) 17457 100
5’ CAGE supported 291 1.67
3’ polyA supported 13456 77.08
Supported Reference Transcript Model (SRTM) 17457 100
Intra-priming 1073 6.15
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 757 -
5’ reference supported (transcript) 116 15.32
3’ reference supported (transcript) 405 53.5
5’ and 3’ reference supported (gene) 100 13.21
5’ reference supported (gene) 217 217
3’ reference supported (gene) 509 67.24
5’ CAGE supported 10 1.32
3’ polyA supported 683 90.22
Supported Reference Transcript Model (SRTM) 169 22.32
Intra-priming 25 3.3
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 361 -
5’ and 3’ reference supported (gene) 241 66.76
5’ reference supported (gene) 315 87.26
3’ reference supported (gene) 278 77.01
5’ CAGE supported 4 1.11
3’ polyA supported 333 92.24
Supported Novel Transcript Model (SNTM) 269 74.52
Intra-priming 3 0.83
Intron retention incidence 40 11.08

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 410 -
5’ and 3’ reference supported (gene) 93 22.68
5’ reference supported (gene) 180 43.9
3’ reference supported (gene) 221 53.9
5’ CAGE supported 4 0.98
3’ polyA supported 336 81.95
Supported Novel Transcript Model (SNTM) 106 25.85
Non-canonical SJ incidence 19 4.63
Full Illumina SJ support 319 77.8
Intra-priming 6 1.46
RT-switching incidence 26 6.34

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 81
True Positive detections (TP) 81
SIRV transcripts associated to TP (Reference Match) 81
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 3
False Positive (FP) 0
Sensitivity 0.96
Precision 1
Non Redundant Precision 1
Positive Detection Rate 0.96
False Discovery Rate 0
False Detection Rate 0
Redundancy 1