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 10341
Number of known genes detected 10289
Number of transcripts detected 20848
Number of transcripts associated to a known gene 20651
Number of unique SJ detected 89023
Absolute value Relative value (%)
Novel SJ 2753 0.03
Non-canonical SJ 414 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 15683 -
Reference Match 15682 99.99
5’ reference supported (transcript) 15682 99.99
3’ reference supported (transcript) 15683 100
5’ reference supported (gene) 15682 99.99
3’ reference supported (gene) 15683 100
5’ CAGE supported 284 1.81
3’ polyA supported 12735 81.2
Supported Reference Transcript Model (SRTM) 15682 99.99
Intra-priming 876 5.59
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1035 -
5’ reference supported (transcript) 439 42.42
3’ reference supported (transcript) 221 21.35
5’ and 3’ reference supported (gene) 216 20.87
5’ reference supported (gene) 642 642
3’ reference supported (gene) 442 42.71
5’ CAGE supported 12 1.16
3’ polyA supported 758 73.24
Supported Reference Transcript Model (SRTM) 459 44.35
Intra-priming 154 14.88
Reference redundancy Level 1.19 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1945 -
5’ and 3’ reference supported (gene) 1313 67.51
5’ reference supported (gene) 1614 82.98
3’ reference supported (gene) 1577 81.08
5’ CAGE supported 20 1.03
3’ polyA supported 1808 92.96
Supported Novel Transcript Model (SNTM) 1440 74.04
Intra-priming 50 2.57
Intron retention incidence 282 14.5

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 1988 -
5’ and 3’ reference supported (gene) 688 34.61
5’ reference supported (gene) 1054 53.02
3’ reference supported (gene) 1308 65.79
5’ CAGE supported 8 0.4
3’ polyA supported 1748 87.93
Supported Novel Transcript Model (SNTM) 641 32.24
Non-canonical SJ incidence 336 16.9
Full Illumina SJ support 1432 72.03
Intra-priming 47 2.36
RT-switching incidence 196 9.86

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 76
True Positive detections (TP) 76
SIRV transcripts associated to TP (Reference Match) 76
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 8
False Positive (FP) 0
Sensitivity 0.9
Precision 1
Non Redundant Precision 1
Positive Detection Rate 0.9
False Discovery Rate 0
False Detection Rate 0
Redundancy 1