Your submission: iso_detect_ref_spectra_ES 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 27449
Number of known genes detected 17650
Number of transcripts detected 134499
Number of transcripts associated to a known gene 121187
Number of unique SJ detected 228080
Absolute value Relative value (%)
Novel SJ 63392 0.28
Non-canonical SJ 16355 0.07

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 29494 -
Reference Match 9718 32.95
5’ reference supported (transcript) 16766 56.85
3’ reference supported (transcript) 16202 54.93
5’ reference supported (gene) 21701 73.58
3’ reference supported (gene) 23370 79.24
5’ CAGE supported 474 1.61
3’ polyA supported 26548 90.01
Supported Reference Transcript Model (SRTM) 20479 69.43
Intra-priming 2661 9.02
Reference redundancy Level 1.05 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 17192 -
5’ reference supported (transcript) 2331 13.56
3’ reference supported (transcript) 9513 55.33
5’ and 3’ reference supported (gene) 1998 11.62
5’ reference supported (gene) 3915 3915
3’ reference supported (gene) 12199 70.96
5’ CAGE supported 124 0.72
3’ polyA supported 15912 92.55
Supported Reference Transcript Model (SRTM) 3407 19.82
Intra-priming 793 4.61
Reference redundancy Level 1.71 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 30432 -
5’ and 3’ reference supported (gene) 20032 65.83
5’ reference supported (gene) 24532 80.61
3’ reference supported (gene) 24692 81.14
5’ CAGE supported 553 1.82
3’ polyA supported 28985 95.25
Supported Novel Transcript Model (SNTM) 19648 64.56
Intra-priming 1335 4.39
Intron retention incidence 15470 50.83

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 44069 -
5’ and 3’ reference supported (gene) 22531 51.13
5’ reference supported (gene) 30298 68.75
3’ reference supported (gene) 31945 72.49
5’ CAGE supported 731 1.66
3’ polyA supported 40797 92.58
Supported Novel Transcript Model (SNTM) 10359 23.51
Non-canonical SJ incidence 10974 24.9
Full Illumina SJ support 16064 36.45
Intra-priming 1865 4.23
RT-switching incidence 3035 6.89

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 286
True Positive detections (TP) 80
SIRV transcripts associated to TP (Reference Match) 80
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 39
False Negative (FN) 4
False Positive (FP) 167
Sensitivity 0.95
Precision 0.28
Non Redundant Precision 0.28
Positive Detection Rate 0.95
False Discovery Rate 0.58
False Detection Rate 0.58
Redundancy 1.49