Your submission: H1_mix_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 6084
Number of known genes detected 6084
Number of transcripts detected 16046
Number of transcripts associated to a known gene 16032
Number of unique SJ detected 52274
Absolute value Relative value (%)
Novel SJ 1024 0.02
Non-canonical SJ 182 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 12859 -
Reference Match 7246 56.35
5’ reference supported (transcript) 11297 87.85
3’ reference supported (transcript) 7927 61.65
5’ reference supported (gene) 12521 97.37
3’ reference supported (gene) 10740 83.52
5’ CAGE supported 10666 82.95
3’ polyA supported 12449 96.81
Supported Reference Transcript Model (SRTM) 12498 97.19
Intra-priming 226 1.76
Reference redundancy Level 1.28 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1001 -
5’ reference supported (transcript) 411 41.06
3’ reference supported (transcript) 328 32.77
5’ and 3’ reference supported (gene) 293 29.27
5’ reference supported (gene) 599 599
3’ reference supported (gene) 599 59.84
5’ CAGE supported 555 55.44
3’ polyA supported 921 92.01
Supported Reference Transcript Model (SRTM) 591 59.04
Intra-priming 74 7.39
Reference redundancy Level 1.14 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1430 -
5’ and 3’ reference supported (gene) 1252 87.55
5’ reference supported (gene) 1401 97.97
3’ reference supported (gene) 1277 89.3
5’ CAGE supported 1274 89.09
3’ polyA supported 1411 98.67
Supported Novel Transcript Model (SNTM) 1313 91.82
Intra-priming 19 1.33
Intron retention incidence 201 14.06

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 742 -
5’ and 3’ reference supported (gene) 451 60.78
5’ reference supported (gene) 583 78.57
3’ reference supported (gene) 574 77.36
5’ CAGE supported 559 75.34
3’ polyA supported 730 98.38
Supported Novel Transcript Model (SNTM) 394 53.1
Non-canonical SJ incidence 130 17.52
Full Illumina SJ support 473 63.75
Intra-priming 6 0.81
RT-switching incidence 52 7.01

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) 63
SIRV transcripts associated to TP (Reference Match) 63
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 21
False Positive (FP) 0
Sensitivity 0.75
Precision 1
Non Redundant Precision 1
Positive Detection Rate 0.75
False Discovery Rate 0
False Detection Rate 0
Redundancy 1