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 12901
Number of known genes detected 12262
Number of transcripts detected 27202
Number of transcripts associated to a known gene 26310
Number of unique SJ detected 130486
Absolute value Relative value (%)
Novel SJ 5429 0.04
Non-canonical SJ 248 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 14371 -
Reference Match 6403 44.56
5’ reference supported (transcript) 9746 67.82
3’ reference supported (transcript) 9267 64.48
5’ reference supported (gene) 12243 85.19
3’ reference supported (gene) 11803 82.13
5’ CAGE supported 313 2.18
3’ polyA motif supported 313 2.18
Supported Reference Transcript Model (SRTM) 10145 70.59
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 3627 -
5’ reference supported (transcript) 647 17.84
3’ reference supported (transcript) 2027 55.89
5’ and 3’ reference supported (gene) 565 15.58
5’ reference supported (gene) 1022 1022
3’ reference supported (gene) 2601 71.71
5’ CAGE supported 24 0.66
3’ polyA motif supported 24 0.66
Supported Reference Transcript Model (SRTM) 567 15.63
Reference redundancy Level 1.18 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 5142 -
5’ and 3’ reference supported (gene) 3409 66.3
5’ reference supported (gene) 4180 81.29
3’ reference supported (gene) 4152 80.75
5’ CAGE supported 114 2.22
3’ polyA motif supported 114 2.22
Supported Novel Transcript Model (SNTM) 3140 61.07
Intron retention incidence 1588 30.88

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 3170 -
5’ and 3’ reference supported (gene) 1347 42.49
5’ reference supported (gene) 1923 60.66
3’ reference supported (gene) 2170 68.45
5’ CAGE supported 52 1.64
3’ polyA motif supported 52 1.64
Supported Novel Transcript Model (SNTM) 885 27.92
Non-canonical SJ incidence 272 8.58
Full Illumina SJ support 2227 70.25
RT-switching incidence 315 9.94

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 13
True Positive detections (TP) 13
SIRV transcripts associated to TP (Reference Match) 13
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 71
False Positive (FP) 0
Sensitivity 0.15
Precision 1
Non Redundant Precision 1
Positive Detection Rate 0.15
False Discovery Rate 0
False Detection Rate 0
Redundancy 1