Your submission: H1_mix_cdna_pacbio_ls on PacBio+Illumina 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 16464
Number of known genes detected 13902
Number of transcripts detected 43746
Number of transcripts associated to a known gene 40749
Number of unique SJ detected 142732
Absolute value Relative value (%)
Novel SJ 5061 0.04
Non-canonical SJ 326 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 28606 -
Reference Match 22726 79.44
5’ reference supported (transcript) 26941 94.18
3’ reference supported (transcript) 23063 80.62
5’ reference supported (gene) 28009 97.91
3’ reference supported (gene) 26191 91.56
5’ CAGE supported 20838 72.84
3’ polyA supported 26319 92.01
Supported Reference Transcript Model (SRTM) 28182 98.52
Intra-priming 573 2
Reference redundancy Level 1.09 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 585 -
5’ reference supported (transcript) 139 23.76
3’ reference supported (transcript) 237 40.51
5’ and 3’ reference supported (gene) 182 31.11
5’ reference supported (gene) 271 271
3’ reference supported (gene) 374 63.93
5’ CAGE supported 256 43.76
3’ polyA supported 519 88.72
Supported Reference Transcript Model (SRTM) 294 50.26
Intra-priming 14 2.39
Reference redundancy Level 1.03 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 8837 -
5’ and 3’ reference supported (gene) 6867 77.71
5’ reference supported (gene) 8109 91.76
3’ reference supported (gene) 7352 83.2
5’ CAGE supported 7575 85.72
3’ polyA supported 8637 97.74
Supported Novel Transcript Model (SNTM) 7455 84.36
Intra-priming 67 0.76
Intron retention incidence 2488 28.15

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 2721 -
5’ and 3’ reference supported (gene) 1572 57.77
5’ reference supported (gene) 2132 78.35
3’ reference supported (gene) 1954 71.81
5’ CAGE supported 2112 77.62
3’ polyA supported 2685 98.68
Supported Novel Transcript Model (SNTM) 2182 80.19
Non-canonical SJ incidence 135 4.96
Full Illumina SJ support 2489 91.47
Intra-priming 23 0.85
RT-switching incidence 182 6.69

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 84
True Positive detections (TP) 84
SIRV transcripts associated to TP (Reference Match) 84
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 0
False Positive (FP) 0
Sensitivity 1
Precision 1
Non Redundant Precision 1
Positive Detection Rate 1
False Discovery Rate 0
False Detection Rate 0
Redundancy 1