Your submission: ES_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 14992
Number of known genes detected 14428
Number of transcripts detected 29979
Number of transcripts associated to a known gene 29284
Number of unique SJ detected 139773
Absolute value Relative value (%)
Novel SJ 1939 0.01
Non-canonical SJ 135 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 26943 -
Reference Match 26942 100
5’ reference supported (transcript) 26942 100
3’ reference supported (transcript) 26943 100
5’ reference supported (gene) 26943 100
3’ reference supported (gene) 26943 100
5’ CAGE supported 414 1.54
3’ polyA supported 20520 76.16
Supported Reference Transcript Model (SRTM) 26943 100
Intra-priming 1668 6.19
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 604 -
5’ reference supported (transcript) 98 16.23
3’ reference supported (transcript) 383 63.41
5’ and 3’ reference supported (gene) 124 20.53
5’ reference supported (gene) 200 200
3’ reference supported (gene) 467 77.32
5’ CAGE supported 6 0.99
3’ polyA supported 548 90.73
Supported Reference Transcript Model (SRTM) 179 29.64
Intra-priming 11 1.82
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1047 -
5’ and 3’ reference supported (gene) 746 71.25
5’ reference supported (gene) 888 84.81
3’ reference supported (gene) 873 83.38
5’ CAGE supported 24 2.29
3’ polyA supported 1000 95.51
Supported Novel Transcript Model (SNTM) 784 74.88
Intra-priming 12 1.15
Intron retention incidence 168 16.05

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 690 -
5’ and 3’ reference supported (gene) 241 34.93
5’ reference supported (gene) 348 50.43
3’ reference supported (gene) 444 64.35
5’ CAGE supported 12 1.74
3’ polyA supported 590 85.51
Supported Novel Transcript Model (SNTM) 191 27.68
Non-canonical SJ incidence 39 5.65
Full Illumina SJ support 484 70.14
Intra-priming 12 1.74
RT-switching incidence 92 13.33

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