Your submission: WTC11_cdna_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 15300
Number of known genes detected 15214
Number of transcripts detected 46409
Number of transcripts associated to a known gene 45970
Number of unique SJ detected 165560
Absolute value Relative value (%)
Novel SJ 5142 0.03
Non-canonical SJ 581 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 34120 -
Reference Match 33570 98.39
5’ reference supported (transcript) 33768 98.97
3’ reference supported (transcript) 33790 99.03
5’ reference supported (gene) 33962 99.54
3’ reference supported (gene) 33937 99.46
5’ CAGE supported 25581 74.97
3’ polyA supported 29074 85.21
Supported Reference Transcript Model (SRTM) 33935 99.46
Intra-priming 805 2.36
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1298 -
5’ reference supported (transcript) 560 43.14
3’ reference supported (transcript) 298 22.96
5’ and 3’ reference supported (gene) 401 30.89
5’ reference supported (gene) 828 828
3’ reference supported (gene) 654 50.39
5’ CAGE supported 833 64.18
3’ polyA supported 1184 91.22
Supported Reference Transcript Model (SRTM) 929 71.57
Intra-priming 45 3.47
Reference redundancy Level 1.16 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 7260 -
5’ and 3’ reference supported (gene) 4676 64.41
5’ reference supported (gene) 5442 74.96
3’ reference supported (gene) 6177 85.08
5’ CAGE supported 4736 65.23
3’ polyA supported 7203 99.21
Supported Novel Transcript Model (SNTM) 5503 75.8
Intra-priming 50 0.69
Intron retention incidence 1816 25.01

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 3292 -
5’ and 3’ reference supported (gene) 1395 42.38
5’ reference supported (gene) 1982 60.21
3’ reference supported (gene) 2307 70.08
5’ CAGE supported 2209 67.1
3’ polyA supported 3256 98.91
Supported Novel Transcript Model (SNTM) 1882 57.17
Non-canonical SJ incidence 511 15.52
Full Illumina SJ support 2431 73.85
Intra-priming 25 0.76
RT-switching incidence 281 8.54

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 81
True Positive detections (TP) 81
SIRV transcripts associated to TP (Reference Match) 81
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 3
False Positive (FP) 0
Sensitivity 0.96
Precision 1
Non Redundant Precision 1
Positive Detection Rate 0.96
False Discovery Rate 0
False Detection Rate 0
Redundancy 1