Your submission: WTC11_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 16630
Number of known genes detected 14113
Number of transcripts detected 46012
Number of transcripts associated to a known gene 43117
Number of unique SJ detected 143382
Absolute value Relative value (%)
Novel SJ 2973 0.02
Non-canonical SJ 344 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 30929 -
Reference Match 24451 79.06
5’ reference supported (transcript) 29061 93.96
3’ reference supported (transcript) 24839 80.31
5’ reference supported (gene) 30279 97.9
3’ reference supported (gene) 28288 91.46
5’ CAGE supported 22387 72.38
3’ polyA supported 28377 91.75
Supported Reference Transcript Model (SRTM) 30505 98.63
Intra-priming 602 1.95
Reference redundancy Level 1.1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 720 -
5’ reference supported (transcript) 162 22.5
3’ reference supported (transcript) 313 43.47
5’ and 3’ reference supported (gene) 199 27.64
5’ reference supported (gene) 311 311
3’ reference supported (gene) 477 66.25
5’ CAGE supported 350 48.61
3’ polyA supported 661 91.81
Supported Reference Transcript Model (SRTM) 384 53.33
Intra-priming 11 1.53
Reference redundancy Level 1.04 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 11332 -
5’ and 3’ reference supported (gene) 8896 78.5
5’ reference supported (gene) 10477 92.45
3’ reference supported (gene) 9472 83.59
5’ CAGE supported 10029 88.5
3’ polyA supported 11124 98.16
Supported Novel Transcript Model (SNTM) 9566 84.42
Intra-priming 114 1.01
Intron retention incidence 3029 26.73

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 136 -
5’ and 3’ reference supported (gene) 59 43.38
5’ reference supported (gene) 78 57.35
3’ reference supported (gene) 104 76.47
5’ CAGE supported 72 52.94
3’ polyA supported 127 93.38
Supported Novel Transcript Model (SNTM) 3 2.21
Non-canonical SJ incidence 132 97.06
Full Illumina SJ support 3 2.21
Intra-priming 7 5.15
RT-switching incidence 76 55.88

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