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 22313
Number of known genes detected 12971
Number of transcripts detected 42495
Number of transcripts associated to a known gene 32914
Number of unique SJ detected 129024
Absolute value Relative value (%)
Novel SJ 1898 0.01
Non-canonical SJ 244 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 23733 -
Reference Match 19205 80.92
5’ reference supported (transcript) 21759 91.68
3’ reference supported (transcript) 19568 82.45
5’ reference supported (gene) 22907 96.52
3’ reference supported (gene) 21427 90.28
5’ CAGE supported 423 1.78
3’ polyA supported 20062 84.53
Supported Reference Transcript Model (SRTM) 22623 95.32
Intra-priming 1079 4.55
Reference redundancy Level 1.11 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 507 -
5’ reference supported (transcript) 88 17.36
3’ reference supported (transcript) 227 44.77
5’ and 3’ reference supported (gene) 111 21.89
5’ reference supported (gene) 176 176
3’ reference supported (gene) 332 65.48
5’ CAGE supported 5 0.99
3’ polyA supported 417 82.25
Supported Reference Transcript Model (SRTM) 166 32.74
Intra-priming 25 4.93
Reference redundancy Level 1.03 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 8674 -
5’ and 3’ reference supported (gene) 6407 73.86
5’ reference supported (gene) 7755 89.41
3’ reference supported (gene) 7080 81.62
5’ CAGE supported 180 2.08
3’ polyA supported 8290 95.57
Supported Novel Transcript Model (SNTM) 6805 78.45
Intra-priming 185 2.13
Intron retention incidence 2770 31.93

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 0 0
5’ and 3’ reference supported (gene) 0 0
5’ reference supported (gene) 0 0
3’ reference supported (gene) 0 0
5’ CAGE supported 0 0
3’ polyA supported 0 0
Supported Novel Transcript Model (SNTM) 0 0
Non-canonical SJ incidence 0 0
Full Illumina SJ support 0 0
Intra-priming 0 0
RT-switching incidence 0 0

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 84
True Positive detections (TP) 84
SIRV transcripts associated to TP (Reference Match) 84
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 0
False Positive (FP) 0
Sensitivity 1
Precision 1
Non Redundant Precision 1
Positive Detection Rate 1
False Discovery Rate 0
False Detection Rate 0
Redundancy 1