Your submission: ES_cdna_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 13817
Number of known genes detected 13767
Number of transcripts detected 33314
Number of transcripts associated to a known gene 32968
Number of unique SJ detected 146880
Absolute value Relative value (%)
Novel SJ 5454 0.04
Non-canonical SJ 1147 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 22733 -
Reference Match 22722 99.95
5’ reference supported (transcript) 22727 99.97
3’ reference supported (transcript) 22726 99.97
5’ reference supported (gene) 22729 99.98
3’ reference supported (gene) 22730 99.99
5’ CAGE supported 384 1.69
3’ polyA supported 18591 81.78
Supported Reference Transcript Model (SRTM) 22729 99.98
Intra-priming 1106 4.87
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 978 -
5’ reference supported (transcript) 369 37.73
3’ reference supported (transcript) 335 34.25
5’ and 3’ reference supported (gene) 261 26.69
5’ reference supported (gene) 533 533
3’ reference supported (gene) 550 56.24
5’ CAGE supported 3 0.31
3’ polyA supported 829 84.76
Supported Reference Transcript Model (SRTM) 456 46.63
Intra-priming 33 3.37
Reference redundancy Level 1.17 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 5240 -
5’ and 3’ reference supported (gene) 3028 57.79
5’ reference supported (gene) 3563 68
3’ reference supported (gene) 4404 84.05
5’ CAGE supported 51 0.97
3’ polyA supported 4989 95.21
Supported Novel Transcript Model (SNTM) 3155 60.21
Intra-priming 77 1.47
Intron retention incidence 1246 23.78

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 4017 -
5’ and 3’ reference supported (gene) 1417 35.28
5’ reference supported (gene) 1968 48.99
3’ reference supported (gene) 2830 70.45
5’ CAGE supported 21 0.52
3’ polyA supported 3577 89.05
Supported Novel Transcript Model (SNTM) 1100 27.38
Non-canonical SJ incidence 965 24.02
Full Illumina SJ support 2552 63.53
Intra-priming 47 1.17
RT-switching incidence 526 13.09

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 80
True Positive detections (TP) 80
SIRV transcripts associated to TP (Reference Match) 80
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 4
False Positive (FP) 0
Sensitivity 0.95
Precision 1
Non Redundant Precision 1
Positive Detection Rate 0.95
False Discovery Rate 0
False Detection Rate 0
Redundancy 1