Your submission: human_H1_mix_PacBio_cDNA_long 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 20612
Number of known genes detected 16379
Number of transcripts detected 60335
Number of transcripts associated to a known gene 55199
Number of unique SJ detected 157861
Absolute value Relative value (%)
Novel SJ 4718 0.03
Non-canonical SJ 849 0.01

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 25111 -
Reference Match 9996 39.81
5’ reference supported (transcript) 17691 70.45
3’ reference supported (transcript) 13938 55.51
5’ reference supported (gene) 21448 85.41
3’ reference supported (gene) 20111 80.09
5’ CAGE supported 20142 80.21
3’ polyA supported 24434 97.3
Supported Reference Transcript Model (SRTM) 22043 87.78
Intra-priming 1434 5.71
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 15267 -
5’ reference supported (transcript) 1428 9.35
3’ reference supported (transcript) 8925 58.46
5’ and 3’ reference supported (gene) 1471 9.64
5’ reference supported (gene) 2638 2638
3’ reference supported (gene) 11459 75.06
5’ CAGE supported 2346 15.37
3’ polyA supported 14690 96.22
Supported Reference Transcript Model (SRTM) 2900 19
Intra-priming 1070 7.01
Reference redundancy Level 1.36 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 13224 -
5’ and 3’ reference supported (gene) 8624 65.21
5’ reference supported (gene) 10682 80.78
3’ reference supported (gene) 10433 78.89
5’ CAGE supported 9976 75.44
3’ polyA supported 12529 94.74
Supported Novel Transcript Model (SNTM) 9543 72.16
Intra-priming 1093 8.27
Intron retention incidence 3608 27.28

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 1597 -
5’ and 3’ reference supported (gene) 734 45.96
5’ reference supported (gene) 1079 67.56
3’ reference supported (gene) 1037 64.93
5’ CAGE supported 1155 72.32
3’ polyA supported 1535 96.12
Supported Novel Transcript Model (SNTM) 849 53.16
Non-canonical SJ incidence 369 23.11
Full Illumina SJ support 1131 70.82
Intra-priming 129 8.08
RT-switching incidence 139 8.7

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 82
True Positive detections (TP) 69
SIRV transcripts associated to TP (Reference Match) 69
Partial True Positive detections (PTP) 6
SIRV transcripts associated to PTP 13
False Negative (FN) 9
False Positive (FP) 0
Sensitivity 0.82
Precision 0.84
Non Redundant Precision 0.84
Positive Detection Rate 0.89
False Discovery Rate 0.07
False Detection Rate 0
Redundancy 1.09