Your submission: WTC11_PacBioOnly 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 18427
Number of known genes detected 13862
Number of transcripts detected 55724
Number of transcripts associated to a known gene 50411
Number of unique SJ detected 140927
Absolute value Relative value (%)
Novel SJ 5434 0.04
Non-canonical SJ 418 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 31713 -
Reference Match 12896 40.66
5’ reference supported (transcript) 22998 72.52
3’ reference supported (transcript) 17729 55.9
5’ reference supported (gene) 27898 87.97
3’ reference supported (gene) 24962 78.71
5’ CAGE supported 27858 87.84
3’ polyA supported 31060 97.94
Supported Reference Transcript Model (SRTM) 29665 93.54
Intra-priming 845 2.66
Reference redundancy Level 1.51 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 3036 -
5’ reference supported (transcript) 1216 40.05
3’ reference supported (transcript) 1372 45.19
5’ and 3’ reference supported (gene) 1023 33.7
5’ reference supported (gene) 1790 1790
3’ reference supported (gene) 2045 67.36
5’ CAGE supported 1985 65.38
3’ polyA supported 2763 91.01
Supported Reference Transcript Model (SRTM) 1959 64.53
Intra-priming 231 7.61
Reference redundancy Level 1.3 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 12635 -
5’ and 3’ reference supported (gene) 9935 78.63
5’ reference supported (gene) 11566 91.54
3’ reference supported (gene) 10764 85.19
5’ CAGE supported 11347 89.81
3’ polyA supported 12318 97.49
Supported Novel Transcript Model (SNTM) 10853 85.9
Intra-priming 419 3.32
Intron retention incidence 3447 27.28

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 3027 -
5’ and 3’ reference supported (gene) 1587 52.43
5’ reference supported (gene) 2189 72.32
3’ reference supported (gene) 2167 71.59
5’ CAGE supported 2550 84.24
3’ polyA supported 2962 97.85
Supported Novel Transcript Model (SNTM) 2318 76.58
Non-canonical SJ incidence 334 11.03
Full Illumina SJ support 2587 85.46
Intra-priming 109 3.6
RT-switching incidence 228 7.53

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 85
True Positive detections (TP) 81
SIRV transcripts associated to TP (Reference Match) 81
Partial True Positive detections (PTP) 1
SIRV transcripts associated to PTP 2
False Negative (FN) 2
False Positive (FP) 2
Sensitivity 0.96
Precision 0.95
Non Redundant Precision 0.95
Positive Detection Rate 0.98
False Discovery Rate 0.04
False Detection Rate 0.02
Redundancy 1.01