Your submission: H1_mix_captrap_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 11405
Number of known genes detected 11314
Number of transcripts detected 30658
Number of transcripts associated to a known gene 30361
Number of unique SJ detected 102883
Absolute value Relative value (%)
Novel SJ 2846 0.03
Non-canonical SJ 376 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 23286 -
Reference Match 22840 98.08
5’ reference supported (transcript) 23034 98.92
3’ reference supported (transcript) 23016 98.84
5’ reference supported (gene) 23179 99.54
3’ reference supported (gene) 23134 99.35
5’ CAGE supported 16897 72.56
3’ polyA supported 19737 84.76
Supported Reference Transcript Model (SRTM) 23118 99.28
Intra-priming 673 2.89
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 2228 -
5’ reference supported (transcript) 1150 51.62
3’ reference supported (transcript) 237 10.64
5’ and 3’ reference supported (gene) 473 21.23
5’ reference supported (gene) 1645 1645
3’ reference supported (gene) 737 33.08
5’ CAGE supported 1093 49.06
3’ polyA supported 1725 77.42
Supported Reference Transcript Model (SRTM) 1310 58.8
Intra-priming 466 20.92
Reference redundancy Level 1.3 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 3013 -
5’ and 3’ reference supported (gene) 2177 72.25
5’ reference supported (gene) 2647 87.85
3’ reference supported (gene) 2477 82.21
5’ CAGE supported 1664 55.23
3’ polyA supported 2897 96.15
Supported Novel Transcript Model (SNTM) 2421 80.35
Intra-priming 133 4.41
Intron retention incidence 421 13.97

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 1834 -
5’ and 3’ reference supported (gene) 641 34.95
5’ reference supported (gene) 1093 59.6
3’ reference supported (gene) 1106 60.31
5’ CAGE supported 800 43.62
3’ polyA supported 1747 95.26
Supported Novel Transcript Model (SNTM) 826 45.04
Non-canonical SJ incidence 287 15.65
Full Illumina SJ support 1361 74.21
Intra-priming 82 4.47
RT-switching incidence 130 7.09

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 74
True Positive detections (TP) 74
SIRV transcripts associated to TP (Reference Match) 74
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 10
False Positive (FP) 0
Sensitivity 0.88
Precision 1
Non Redundant Precision 1
Positive Detection Rate 0.88
False Discovery Rate 0
False Detection Rate 0
Redundancy 1