Your submission: iso_detect_ref_spectra_WTC11 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 30252
Number of known genes detected 21317
Number of transcripts detected 174183
Number of transcripts associated to a known gene 159183
Number of unique SJ detected 282405
Absolute value Relative value (%)
Novel SJ 81663 0.29
Non-canonical SJ 19867 0.07

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 46521 -
Reference Match 14254 30.64
5’ reference supported (transcript) 26794 57.6
3’ reference supported (transcript) 23714 50.97
5’ reference supported (gene) 34792 74.79
3’ reference supported (gene) 37530 80.67
5’ CAGE supported 32549 69.97
3’ polyA supported 44902 96.52
Supported Reference Transcript Model (SRTM) 36688 78.86
Intra-priming 3324 7.15
Reference redundancy Level 1.05 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 18864 -
5’ reference supported (transcript) 3105 16.46
3’ reference supported (transcript) 9619 50.99
5’ and 3’ reference supported (gene) 2926 15.51
5’ reference supported (gene) 5254 5254
3’ reference supported (gene) 13553 71.85
5’ CAGE supported 6355 33.69
3’ polyA supported 18403 97.56
Supported Reference Transcript Model (SRTM) 7432 39.4
Intra-priming 738 3.91
Reference redundancy Level 1.53 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 43152 -
5’ and 3’ reference supported (gene) 30476 70.62
5’ reference supported (gene) 36341 84.22
3’ reference supported (gene) 35778 82.91
5’ CAGE supported 34918 80.92
3’ polyA supported 42476 98.43
Supported Novel Transcript Model (SNTM) 29601 68.6
Intra-priming 1535 3.56
Intron retention incidence 18628 43.17

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 50646 -
5’ and 3’ reference supported (gene) 28075 55.43
5’ reference supported (gene) 37957 74.95
3’ reference supported (gene) 36110 71.3
5’ CAGE supported 39474 77.94
3’ polyA supported 49595 97.92
Supported Novel Transcript Model (SNTM) 16657 32.89
Non-canonical SJ incidence 9886 19.52
Full Illumina SJ support 19750 39
Intra-priming 2031 4.01
RT-switching incidence 2784 5.5

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 277
True Positive detections (TP) 80
SIRV transcripts associated to TP (Reference Match) 80
Partial True Positive detections (PTP) 1
SIRV transcripts associated to PTP 40
False Negative (FN) 3
False Positive (FP) 157
Sensitivity 0.95
Precision 0.29
Non Redundant Precision 0.29
Positive Detection Rate 0.96
False Discovery Rate 0.57
False Detection Rate 0.57
Redundancy 1.48