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 3164
Number of known genes detected 3076
Number of transcripts detected 4384
Number of transcripts associated to a known gene 4151
Number of unique SJ detected 15581
Absolute value Relative value (%)
Novel SJ 572 0.04
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 2080 -
Reference Match 1050 50.48
5’ reference supported (transcript) 1615 77.64
3’ reference supported (transcript) 1362 65.48
5’ reference supported (gene) 1881 90.43
3’ reference supported (gene) 1827 87.84
5’ CAGE supported 1644 79.04
3’ polyA supported 2035 97.84
Supported Reference Transcript Model (SRTM) 1905 91.59
Intra-priming 9 0.43
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1114 -
5’ reference supported (transcript) 123 11.04
3’ reference supported (transcript) 677 60.77
5’ and 3’ reference supported (gene) 108 9.69
5’ reference supported (gene) 181 181
3’ reference supported (gene) 887 79.62
5’ CAGE supported 191 17.15
3’ polyA supported 1086 97.49
Supported Reference Transcript Model (SRTM) 207 18.58
Intra-priming 6 0.54
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 623 -
5’ and 3’ reference supported (gene) 457 73.35
5’ reference supported (gene) 493 79.13
3’ reference supported (gene) 565 90.69
5’ CAGE supported 468 75.12
3’ polyA supported 619 99.36
Supported Novel Transcript Model (SNTM) 481 77.21
Intra-priming 2 0.32
Intron retention incidence 134 21.51

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 334 -
5’ and 3’ reference supported (gene) 212 63.47
5’ reference supported (gene) 258 77.25
3’ reference supported (gene) 260 77.84
5’ CAGE supported 258 77.25
3’ polyA supported 331 99.1
Supported Novel Transcript Model (SNTM) 242 72.46
Non-canonical SJ incidence 0 0
Full Illumina SJ support 281 84.13
Intra-priming 0 0
RT-switching incidence 22 6.59

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 53
True Positive detections (TP) 44
SIRV transcripts associated to TP (Reference Match) 44
Partial True Positive detections (PTP) 7
SIRV transcripts associated to PTP 7
False Negative (FN) 33
False Positive (FP) 2
Sensitivity 0.52
Precision 0.83
Non Redundant Precision 0.83
Positive Detection Rate 0.61
False Discovery Rate 0.17
False Detection Rate 0.04
Redundancy 1