Your submission: WTC11_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 5796
Number of known genes detected 5796
Number of transcripts detected 15553
Number of transcripts associated to a known gene 15540
Number of unique SJ detected 47349
Absolute value Relative value (%)
Novel SJ 1157 0.02
Non-canonical SJ 190 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 12553 -
Reference Match 7007 55.82
5’ reference supported (transcript) 11055 88.07
3’ reference supported (transcript) 7682 61.2
5’ reference supported (gene) 12262 97.68
3’ reference supported (gene) 10468 83.39
5’ CAGE supported 10682 85.1
3’ polyA supported 12211 97.28
Supported Reference Transcript Model (SRTM) 12233 97.45
Intra-priming 163 1.3
Reference redundancy Level 1.27 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 703 -
5’ reference supported (transcript) 316 44.95
3’ reference supported (transcript) 226 32.15
5’ and 3’ reference supported (gene) 257 36.56
5’ reference supported (gene) 478 478
3’ reference supported (gene) 431 61.31
5’ CAGE supported 503 71.55
3’ polyA supported 658 93.6
Supported Reference Transcript Model (SRTM) 551 78.38
Intra-priming 42 5.97
Reference redundancy Level 1.11 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1449 -
5’ and 3’ reference supported (gene) 1278 88.2
5’ reference supported (gene) 1415 97.65
3’ reference supported (gene) 1309 90.34
5’ CAGE supported 1301 89.79
3’ polyA supported 1438 99.24
Supported Novel Transcript Model (SNTM) 1326 91.51
Intra-priming 13 0.9
Intron retention incidence 181 12.49

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 835 -
5’ and 3’ reference supported (gene) 524 62.75
5’ reference supported (gene) 682 81.68
3’ reference supported (gene) 642 76.89
5’ CAGE supported 715 85.63
3’ polyA supported 825 98.8
Supported Novel Transcript Model (SNTM) 546 65.39
Non-canonical SJ incidence 125 14.97
Full Illumina SJ support 579 69.34
Intra-priming 8 0.96
RT-switching incidence 54 6.47

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 63
True Positive detections (TP) 62
SIRV transcripts associated to TP (Reference Match) 62
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 22
False Positive (FP) 1
Sensitivity 0.74
Precision 0.98
Non Redundant Precision 0.98
Positive Detection Rate 0.74
False Discovery Rate 0.02
False Detection Rate 0.02
Redundancy 1