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 16893
Number of known genes detected 16456
Number of transcripts detected 45990
Number of transcripts associated to a known gene 45373
Number of unique SJ detected 160957
Absolute value Relative value (%)
Novel SJ 1771 0.01
Non-canonical SJ 110 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 42403 -
Reference Match 41877 98.76
5’ reference supported (transcript) 42073 99.22
3’ reference supported (transcript) 42085 99.25
5’ reference supported (gene) 42236 99.61
3’ reference supported (gene) 42196 99.51
5’ CAGE supported 27466 64.77
3’ polyA supported 34413 81.16
Supported Reference Transcript Model (SRTM) 42178 99.47
Intra-priming 1140 2.69
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 874 -
5’ reference supported (transcript) 175 20.02
3’ reference supported (transcript) 466 53.32
5’ and 3’ reference supported (gene) 220 25.17
5’ reference supported (gene) 353 353
3’ reference supported (gene) 644 73.68
5’ CAGE supported 456 52.17
3’ polyA supported 822 94.05
Supported Reference Transcript Model (SRTM) 504 57.67
Intra-priming 11 1.26
Reference redundancy Level 1.03 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1442 -
5’ and 3’ reference supported (gene) 1065 73.86
5’ reference supported (gene) 1255 87.03
3’ reference supported (gene) 1224 84.88
5’ CAGE supported 1263 87.59
3’ polyA supported 1428 99.03
Supported Novel Transcript Model (SNTM) 1248 86.55
Intra-priming 9 0.62
Intron retention incidence 303 21.01

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 654 -
5’ and 3’ reference supported (gene) 268 40.98
5’ reference supported (gene) 384 58.72
3’ reference supported (gene) 418 63.91
5’ CAGE supported 533 81.5
3’ polyA supported 638 97.55
Supported Novel Transcript Model (SNTM) 456 69.72
Non-canonical SJ incidence 40 6.12
Full Illumina SJ support 529 80.89
Intra-priming 9 1.38
RT-switching incidence 58 8.87

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 81
True Positive detections (TP) 81
SIRV transcripts associated to TP (Reference Match) 81
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 3
False Positive (FP) 0
Sensitivity 0.96
Precision 1
Non Redundant Precision 1
Positive Detection Rate 0.96
False Discovery Rate 0
False Detection Rate 0
Redundancy 1