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 5378
Number of known genes detected 5378
Number of transcripts detected 11747
Number of transcripts associated to a known gene 11708
Number of unique SJ detected 44319
Absolute value Relative value (%)
Novel SJ 1158 0.03
Non-canonical SJ 220 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 9302 -
Reference Match 4999 53.74
5’ reference supported (transcript) 7256 78
3’ reference supported (transcript) 5823 62.6
5’ reference supported (gene) 8830 94.93
3’ reference supported (gene) 7320 78.69
5’ CAGE supported 178 1.91
3’ polyA supported 8785 94.44
Supported Reference Transcript Model (SRTM) 8517 91.56
Intra-priming 188 2.02
Reference redundancy Level 1.3 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 513 -
5’ reference supported (transcript) 147 28.65
3’ reference supported (transcript) 241 46.98
5’ and 3’ reference supported (gene) 154 30.02
5’ reference supported (gene) 265 265
3’ reference supported (gene) 350 68.23
5’ CAGE supported 8 1.56
3’ polyA supported 456 88.89
Supported Reference Transcript Model (SRTM) 216 42.11
Intra-priming 20 3.9
Reference redundancy Level 1.11 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 944 -
5’ and 3’ reference supported (gene) 779 82.52
5’ reference supported (gene) 909 96.29
3’ reference supported (gene) 810 85.81
5’ CAGE supported 13 1.38
3’ polyA supported 911 96.5
Supported Novel Transcript Model (SNTM) 833 88.24
Intra-priming 5 0.53
Intron retention incidence 173 18.33

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 949 -
5’ and 3’ reference supported (gene) 491 51.74
5’ reference supported (gene) 674 71.02
3’ reference supported (gene) 664 69.97
5’ CAGE supported 9 0.95
3’ polyA supported 858 90.41
Supported Novel Transcript Model (SNTM) 381 40.15
Non-canonical SJ incidence 180 18.97
Full Illumina SJ support 634 66.81
Intra-priming 19 2
RT-switching incidence 87 9.17

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 63
True Positive detections (TP) 62
SIRV transcripts associated to TP (Reference Match) 62
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 22
False Positive (FP) 1
Sensitivity 0.74
Precision 0.98
Non Redundant Precision 0.98
Positive Detection Rate 0.74
False Discovery Rate 0.02
False Detection Rate 0.02
Redundancy 1