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 12462
Number of known genes detected 6473
Number of transcripts detected 15379
Number of transcripts associated to a known gene 9292
Number of unique SJ detected 62570
Absolute value Relative value (%)
Novel SJ 1273 0.02
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 6612 -
Reference Match 3467 52.43
5’ reference supported (transcript) 4842 73.23
3’ reference supported (transcript) 4692 70.96
5’ reference supported (gene) 5772 87.3
3’ reference supported (gene) 5617 84.95
5’ CAGE supported 121 1.83
3’ polyA supported 6364 96.25
Supported Reference Transcript Model (SRTM) 5630 85.15
Intra-priming 12 0.18
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 395 -
5’ reference supported (transcript) 104 26.33
3’ reference supported (transcript) 211 53.42
5’ and 3’ reference supported (gene) 123 31.14
5’ reference supported (gene) 169 169
3’ reference supported (gene) 275 69.62
5’ CAGE supported 3 0.76
3’ polyA supported 327 82.78
Supported Reference Transcript Model (SRTM) 157 39.75
Intra-priming 4 1.01
Reference redundancy Level 1.04 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1480 -
5’ and 3’ reference supported (gene) 1230 83.11
5’ reference supported (gene) 1352 91.35
3’ reference supported (gene) 1329 89.8
5’ CAGE supported 30 2.03
3’ polyA supported 1427 96.42
Supported Novel Transcript Model (SNTM) 1253 84.66
Intra-priming 2 0.14
Intron retention incidence 463 31.28

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 805 -
5’ and 3’ reference supported (gene) 423 52.55
5’ reference supported (gene) 517 64.22
3’ reference supported (gene) 647 80.37
5’ CAGE supported 15 1.86
3’ polyA supported 761 94.53
Supported Novel Transcript Model (SNTM) 392 48.7
Non-canonical SJ incidence 0 0
Full Illumina SJ support 652 80.99
Intra-priming 1 0.12
RT-switching incidence 78 9.69

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) 74
SIRV transcripts associated to TP (Reference Match) 74
Partial True Positive detections (PTP) 2
SIRV transcripts associated to PTP 2
False Negative (FN) 8
False Positive (FP) 5
Sensitivity 0.88
Precision 0.91
Non Redundant Precision 0.91
Positive Detection Rate 0.9
False Discovery Rate 0.09
False Detection Rate 0.06
Redundancy 1