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 10983
Number of known genes detected 10900
Number of transcripts detected 29010
Number of transcripts associated to a known gene 28735
Number of unique SJ detected 94186
Absolute value Relative value (%)
Novel SJ 2976 0.03
Non-canonical SJ 355 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 22396 -
Reference Match 21965 98.08
5’ reference supported (transcript) 22130 98.81
3’ reference supported (transcript) 22149 98.9
5’ reference supported (gene) 22287 99.51
3’ reference supported (gene) 22251 99.35
5’ CAGE supported 17283 77.17
3’ polyA supported 19092 85.25
Supported Reference Transcript Model (SRTM) 22244 99.32
Intra-priming 562 2.51
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1623 -
5’ reference supported (transcript) 876 53.97
3’ reference supported (transcript) 183 11.28
5’ and 3’ reference supported (gene) 359 22.12
5’ reference supported (gene) 1237 1237
3’ reference supported (gene) 566 34.87
5’ CAGE supported 1193 73.51
3’ polyA supported 1353 83.36
Supported Reference Transcript Model (SRTM) 1170 72.09
Intra-priming 255 15.71
Reference redundancy Level 1.21 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 2844 -
5’ and 3’ reference supported (gene) 2122 74.61
5’ reference supported (gene) 2509 88.22
3’ reference supported (gene) 2397 84.28
5’ CAGE supported 2132 74.96
3’ polyA supported 2779 97.71
Supported Novel Transcript Model (SNTM) 2384 83.83
Intra-priming 81 2.85
Intron retention incidence 335 11.78

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 1872 -
5’ and 3’ reference supported (gene) 654 34.94
5’ reference supported (gene) 1139 60.84
3’ reference supported (gene) 1105 59.03
5’ CAGE supported 1256 67.09
3’ polyA supported 1817 97.06
Supported Novel Transcript Model (SNTM) 1031 55.07
Non-canonical SJ incidence 279 14.9
Full Illumina SJ support 1360 72.65
Intra-priming 50 2.67
RT-switching incidence 111 5.93

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 70
True Positive detections (TP) 70
SIRV transcripts associated to TP (Reference Match) 70
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 14
False Positive (FP) 0
Sensitivity 0.83
Precision 1
Non Redundant Precision 1
Positive Detection Rate 0.83
False Discovery Rate 0
False Detection Rate 0
Redundancy 1