Your submission: ES_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 2578
Number of known genes detected 2169
Number of transcripts detected 3134
Number of transcripts associated to a known gene 2604
Number of unique SJ detected 11265
Absolute value Relative value (%)
Novel SJ 527 0.05
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 1369 -
Reference Match 713 52.08
5’ reference supported (transcript) 1015 74.14
3’ reference supported (transcript) 937 68.44
5’ reference supported (gene) 1191 87
3’ reference supported (gene) 1124 82.1
5’ CAGE supported 31 2.26
3’ polyA supported 1290 94.23
Supported Reference Transcript Model (SRTM) 1149 83.93
Intra-priming 10 0.73
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 554 -
5’ reference supported (transcript) 43 7.76
3’ reference supported (transcript) 350 63.18
5’ and 3’ reference supported (gene) 46 8.3
5’ reference supported (gene) 72 72
3’ reference supported (gene) 435 78.52
5’ CAGE supported 3 0.54
3’ polyA supported 531 95.85
Supported Reference Transcript Model (SRTM) 60 10.83
Intra-priming 2 0.36
Reference redundancy Level 1.01 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 364 -
5’ and 3’ reference supported (gene) 269 73.9
5’ reference supported (gene) 294 80.77
3’ reference supported (gene) 324 89.01
5’ CAGE supported 0 0
3’ polyA supported 356 97.8
Supported Novel Transcript Model (SNTM) 276 75.82
Intra-priming 0 0
Intron retention incidence 119 32.69

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 317 -
5’ and 3’ reference supported (gene) 159 50.16
5’ reference supported (gene) 220 69.4
3’ reference supported (gene) 222 70.03
5’ CAGE supported 2 0.63
3’ polyA supported 287 90.54
Supported Novel Transcript Model (SNTM) 163 51.42
Non-canonical SJ incidence 0 0
Full Illumina SJ support 255 80.44
Intra-priming 0 0
RT-switching incidence 26 8.2

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 57
True Positive detections (TP) 44
SIRV transcripts associated to TP (Reference Match) 44
Partial True Positive detections (PTP) 6
SIRV transcripts associated to PTP 7
False Negative (FN) 34
False Positive (FP) 6
Sensitivity 0.52
Precision 0.77
Non Redundant Precision 0.77
Positive Detection Rate 0.6
False Discovery Rate 0.21
False Detection Rate 0.11
Redundancy 1.02