Your submission: H1_mix_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 4209
Number of known genes detected 4171
Number of transcripts detected 4770
Number of transcripts associated to a known gene 4730
Number of unique SJ detected 2931
Absolute value Relative value (%)
Novel SJ 44 0.02
Non-canonical SJ 18 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 4659 -
Reference Match 4622 99.21
5’ reference supported (transcript) 4633 99.44
3’ reference supported (transcript) 4637 99.53
5’ reference supported (gene) 4640 99.59
3’ reference supported (gene) 4640 99.59
5’ CAGE supported 1125 24.15
3’ polyA supported 2882 61.86
Supported Reference Transcript Model (SRTM) 4635 99.48
Intra-priming 231 4.96
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 62 -
5’ reference supported (transcript) 8 12.9
3’ reference supported (transcript) 30 48.39
5’ and 3’ reference supported (gene) 3 4.84
5’ reference supported (gene) 13 13
3’ reference supported (gene) 37 59.68
5’ CAGE supported 6 9.68
3’ polyA supported 46 74.19
Supported Reference Transcript Model (SRTM) 6 9.68
Intra-priming 0 0
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 6 -
5’ and 3’ reference supported (gene) 0 0
5’ reference supported (gene) 1 16.67
3’ reference supported (gene) 1 16.67
5’ CAGE supported 0 0
3’ polyA supported 4 66.67
Supported Novel Transcript Model (SNTM) 0 0
Intra-priming 0 0
Intron retention incidence 1 16.67

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 3 -
5’ and 3’ reference supported (gene) 0 0
5’ reference supported (gene) 0 0
3’ reference supported (gene) 1 33.33
5’ CAGE supported 0 0
3’ polyA supported 1 33.33
Supported Novel Transcript Model (SNTM) 0 0
Non-canonical SJ incidence 0 0
Full Illumina SJ support 2 66.67
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 28
True Positive detections (TP) 28
SIRV transcripts associated to TP (Reference Match) 28
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 56
False Positive (FP) 0
Sensitivity 0.33
Precision 1
Non Redundant Precision 1
Positive Detection Rate 0.33
False Discovery Rate 0
False Detection Rate 0
Redundancy 1