Your submission: mouse_ES_PacBio_cDNA_long 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 24951
Number of known genes detected 14810
Number of transcripts detected 53777
Number of transcripts associated to a known gene 42848
Number of unique SJ detected 142605
Absolute value Relative value (%)
Novel SJ 4766 0.03
Non-canonical SJ 1121 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 19262 -
Reference Match 7388 38.36
5’ reference supported (transcript) 12198 63.33
3’ reference supported (transcript) 11403 59.2
5’ reference supported (gene) 15807 82.06
3’ reference supported (gene) 15013 77.94
5’ CAGE supported 439 2.28
3’ polyA supported 17743 92.11
Supported Reference Transcript Model (SRTM) 15131 78.55
Intra-priming 1596 8.29
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 12308 -
5’ reference supported (transcript) 958 7.78
3’ reference supported (transcript) 7876 63.99
5’ and 3’ reference supported (gene) 1009 8.2
5’ reference supported (gene) 1751 1751
3’ reference supported (gene) 9473 76.97
5’ CAGE supported 53 0.43
3’ polyA supported 11246 91.37
Supported Reference Transcript Model (SRTM) 1538 12.5
Intra-priming 855 6.95
Reference redundancy Level 1.42 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 8977 -
5’ and 3’ reference supported (gene) 5788 64.48
5’ reference supported (gene) 7208 80.29
3’ reference supported (gene) 7127 79.39
5’ CAGE supported 168 1.87
3’ polyA supported 8132 90.59
Supported Novel Transcript Model (SNTM) 5994 66.77
Intra-priming 820 9.13
Intron retention incidence 2419 26.95

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 2301 -
5’ and 3’ reference supported (gene) 925 40.2
5’ reference supported (gene) 1370 59.54
3’ reference supported (gene) 1530 66.49
5’ CAGE supported 34 1.48
3’ polyA supported 2002 87.01
Supported Novel Transcript Model (SNTM) 728 31.64
Non-canonical SJ incidence 566 24.6
Full Illumina SJ support 1505 65.41
Intra-priming 171 7.43
RT-switching incidence 276 11.99

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 82
True Positive detections (TP) 69
SIRV transcripts associated to TP (Reference Match) 69
Partial True Positive detections (PTP) 7
SIRV transcripts associated to PTP 13
False Negative (FN) 8
False Positive (FP) 0
Sensitivity 0.82
Precision 0.84
Non Redundant Precision 0.84
Positive Detection Rate 0.9
False Discovery Rate 0.09
False Detection Rate 0
Redundancy 1.08