Your submission: human_H1_mix_cDNA_pb 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 51638
Number of known genes detected 18766
Number of transcripts detected 211516
Number of transcripts associated to a known gene 164118
Number of unique SJ detected 268271
Absolute value Relative value (%)
Novel SJ 98503 0.37
Non-canonical SJ 31474 0.12

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 33370 -
Reference Match 5254 15.74
5’ reference supported (transcript) 19297 57.83
3’ reference supported (transcript) 9769 29.27
5’ reference supported (gene) 24772 74.23
3’ reference supported (gene) 16347 48.99
5’ CAGE supported 21685 64.98
3’ polyA supported 30864 92.49
Supported Reference Transcript Model (SRTM) 24774 74.24
Intra-priming 229 0.69
Reference redundancy Level 1.72 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 12726 -
5’ reference supported (transcript) 4118 32.36
3’ reference supported (transcript) 3271 25.7
5’ and 3’ reference supported (gene) 1823 14.33
5’ reference supported (gene) 5716 5716
3’ reference supported (gene) 5379 42.27
5’ CAGE supported 5135 40.35
3’ polyA supported 10752 84.49
Supported Reference Transcript Model (SRTM) 4962 38.99
Intra-priming 296 2.33
Reference redundancy Level 1.4 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 55599 -
5’ and 3’ reference supported (gene) 29432 52.94
5’ reference supported (gene) 40549 72.93
3’ reference supported (gene) 38554 69.34
5’ CAGE supported 36327 65.34
3’ polyA supported 52010 93.54
Supported Novel Transcript Model (SNTM) 31931 57.43
Intra-priming 591 1.06
Intron retention incidence 25947 46.67

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 62423 -
5’ and 3’ reference supported (gene) 28477 45.62
5’ reference supported (gene) 42338 67.82
3’ reference supported (gene) 40496 64.87
5’ CAGE supported 39864 63.86
3’ polyA supported 59401 95.16
Supported Novel Transcript Model (SNTM) 13797 22.1
Non-canonical SJ incidence 18342 29.38
Full Illumina SJ support 19100 30.6
Intra-priming 695 1.11
RT-switching incidence 3688 5.91

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 150
True Positive detections (TP) 21
SIRV transcripts associated to TP (Reference Match) 21
Partial True Positive detections (PTP) 1
SIRV transcripts associated to PTP 70
False Negative (FN) 62
False Positive (FP) 59
Sensitivity 0.25
Precision 0.14
Non Redundant Precision 0.14
Positive Detection Rate 0.26
False Discovery Rate 0.4
False Detection Rate 0.39
Redundancy 4.14