Your submission: H1_mix_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 15469
Number of known genes detected 13589
Number of transcripts detected 37756
Number of transcripts associated to a known gene 35624
Number of unique SJ detected 136016
Absolute value Relative value (%)
Novel SJ 1671 0.01
Non-canonical SJ 321 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 27942 -
Reference Match 22668 81.13
5’ reference supported (transcript) 26493 94.81
3’ reference supported (transcript) 22958 82.16
5’ reference supported (gene) 27438 98.2
3’ reference supported (gene) 25782 92.27
5’ CAGE supported 20300 72.65
3’ polyA supported 25682 91.91
Supported Reference Transcript Model (SRTM) 27599 98.77
Intra-priming 556 1.99
Reference redundancy Level 1.08 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 505 -
5’ reference supported (transcript) 117 23.17
3’ reference supported (transcript) 209 41.39
5’ and 3’ reference supported (gene) 156 30.89
5’ reference supported (gene) 228 228
3’ reference supported (gene) 331 65.54
5’ CAGE supported 229 45.35
3’ polyA supported 453 89.7
Supported Reference Transcript Model (SRTM) 256 50.69
Intra-priming 9 1.78
Reference redundancy Level 1.03 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 7059 -
5’ and 3’ reference supported (gene) 5488 77.74
5’ reference supported (gene) 6491 91.95
3’ reference supported (gene) 5871 83.17
5’ CAGE supported 6083 86.17
3’ polyA supported 6908 97.86
Supported Novel Transcript Model (SNTM) 5996 84.94
Intra-priming 58 0.82
Intron retention incidence 1938 27.45

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 118 -
5’ and 3’ reference supported (gene) 51 43.22
5’ reference supported (gene) 68 57.63
3’ reference supported (gene) 87 73.73
5’ CAGE supported 49 41.53
3’ polyA supported 109 92.37
Supported Novel Transcript Model (SNTM) 1 0.85
Non-canonical SJ incidence 116 98.31
Full Illumina SJ support 1 0.85
Intra-priming 8 6.78
RT-switching incidence 69 58.47

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