Your submission: human_WTC11_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 21182
Number of known genes detected 16731
Number of transcripts detected 62938
Number of transcripts associated to a known gene 57541
Number of unique SJ detected 158087
Absolute value Relative value (%)
Novel SJ 4981 0.03
Non-canonical SJ 848 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 25561 -
Reference Match 10233 40.03
5’ reference supported (transcript) 18027 70.53
3’ reference supported (transcript) 14263 55.8
5’ reference supported (gene) 21777 85.2
3’ reference supported (gene) 20472 80.09
5’ CAGE supported 20888 81.72
3’ polyA supported 24878 97.33
Supported Reference Transcript Model (SRTM) 22617 88.48
Intra-priming 1488 5.82
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 17248 -
5’ reference supported (transcript) 1401 8.12
3’ reference supported (transcript) 10243 59.39
5’ and 3’ reference supported (gene) 1567 9.09
5’ reference supported (gene) 2686 2686
3’ reference supported (gene) 13166 76.33
5’ CAGE supported 3431 19.89
3’ polyA supported 16720 96.94
Supported Reference Transcript Model (SRTM) 3982 23.09
Intra-priming 1059 6.14
Reference redundancy Level 1.39 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 13003 -
5’ and 3’ reference supported (gene) 8418 64.74
5’ reference supported (gene) 10474 80.55
3’ reference supported (gene) 10226 78.64
5’ CAGE supported 10261 78.91
3’ polyA supported 12366 95.1
Supported Novel Transcript Model (SNTM) 9485 72.94
Intra-priming 1105 8.5
Intron retention incidence 3205 24.65

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 1729 -
5’ and 3’ reference supported (gene) 799 46.21
5’ reference supported (gene) 1186 68.59
3’ reference supported (gene) 1121 64.84
5’ CAGE supported 1440 83.29
3’ polyA supported 1668 96.47
Supported Novel Transcript Model (SNTM) 1075 62.17
Non-canonical SJ incidence 363 20.99
Full Illumina SJ support 1254 72.53
Intra-priming 138 7.98
RT-switching incidence 120 6.94

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 79
True Positive detections (TP) 68
SIRV transcripts associated to TP (Reference Match) 68
Partial True Positive detections (PTP) 6
SIRV transcripts associated to PTP 11
False Negative (FN) 10
False Positive (FP) 0
Sensitivity 0.81
Precision 0.86
Non Redundant Precision 0.86
Positive Detection Rate 0.88
False Discovery Rate 0.08
False Detection Rate 0
Redundancy 1.07