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 12717
Number of known genes detected 12431
Number of transcripts detected 30227
Number of transcripts associated to a known gene 29873
Number of unique SJ detected 93852
Absolute value Relative value (%)
Novel SJ 883 0.01
Non-canonical SJ 68 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 28107 -
Reference Match 27693 98.53
5’ reference supported (transcript) 27863 99.13
3’ reference supported (transcript) 27852 99.09
5’ reference supported (gene) 27990 99.58
3’ reference supported (gene) 27936 99.39
5’ CAGE supported 18509 65.85
3’ polyA supported 22899 81.47
Supported Reference Transcript Model (SRTM) 27920 99.33
Intra-priming 787 2.8
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1080 -
5’ reference supported (transcript) 235 21.76
3’ reference supported (transcript) 469 43.43
5’ and 3’ reference supported (gene) 191 17.69
5’ reference supported (gene) 417 417
3’ reference supported (gene) 695 64.35
5’ CAGE supported 381 35.28
3’ polyA supported 1002 92.78
Supported Reference Transcript Model (SRTM) 413 38.24
Intra-priming 49 4.54
Reference redundancy Level 1.03 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 429 -
5’ and 3’ reference supported (gene) 311 72.49
5’ reference supported (gene) 391 91.14
3’ reference supported (gene) 340 79.25
5’ CAGE supported 344 80.19
3’ polyA supported 419 97.67
Supported Novel Transcript Model (SNTM) 366 85.31
Intra-priming 4 0.93
Intron retention incidence 60 13.99

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 257 -
5’ and 3’ reference supported (gene) 69 26.85
5’ reference supported (gene) 136 52.92
3’ reference supported (gene) 135 52.53
5’ CAGE supported 135 52.53
3’ polyA supported 252 98.05
Supported Novel Transcript Model (SNTM) 133 51.75
Non-canonical SJ incidence 22 8.56
Full Illumina SJ support 217 84.44
Intra-priming 4 1.56
RT-switching incidence 18 7

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 82
True Positive detections (TP) 80
SIRV transcripts associated to TP (Reference Match) 80
Partial True Positive detections (PTP) 1
SIRV transcripts associated to PTP 2
False Negative (FN) 3
False Positive (FP) 0
Sensitivity 0.95
Precision 0.98
Non Redundant Precision 0.98
Positive Detection Rate 0.96
False Discovery Rate 0.01
False Detection Rate 0
Redundancy 1.01