Your submission: mouse_ES_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 54371
Number of known genes detected 18631
Number of transcripts detected 282529
Number of transcripts associated to a known gene 236517
Number of unique SJ detected 290480
Absolute value Relative value (%)
Novel SJ 127147 0.44
Non-canonical SJ 35568 0.12

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 44371 -
Reference Match 8356 18.83
5’ reference supported (transcript) 25708 57.94
3’ reference supported (transcript) 14553 32.8
5’ reference supported (gene) 32772 73.86
3’ reference supported (gene) 21619 48.72
5’ CAGE supported 905 2.04
3’ polyA supported 36065 81.28
Supported Reference Transcript Model (SRTM) 27162 61.22
Intra-priming 1967 4.43
Reference redundancy Level 1.96 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 18089 -
5’ reference supported (transcript) 5290 29.24
3’ reference supported (transcript) 6238 34.49
5’ and 3’ reference supported (gene) 2833 15.66
5’ reference supported (gene) 7475 7475
3’ reference supported (gene) 8861 48.99
5’ CAGE supported 208 1.15
3’ polyA supported 14043 77.63
Supported Reference Transcript Model (SRTM) 5584 30.87
Intra-priming 1529 8.45
Reference redundancy Level 1.67 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 70282 -
5’ and 3’ reference supported (gene) 38864 55.3
5’ reference supported (gene) 52387 74.54
3’ reference supported (gene) 51212 72.87
5’ CAGE supported 1207 1.72
3’ polyA supported 63670 90.59
Supported Novel Transcript Model (SNTM) 39953 56.85
Intra-priming 3558 5.06
Intron retention incidence 38189 54.34

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 103775 -
5’ and 3’ reference supported (gene) 47777 46.04
5’ reference supported (gene) 68062 65.59
3’ reference supported (gene) 71109 68.52
5’ CAGE supported 1729 1.67
3’ polyA supported 93565 90.16
Supported Novel Transcript Model (SNTM) 18497 17.82
Non-canonical SJ incidence 30825 29.7
Full Illumina SJ support 31356 30.22
Intra-priming 5020 4.84
RT-switching incidence 5770 5.56

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 365
True Positive detections (TP) 79
SIRV transcripts associated to TP (Reference Match) 79
Partial True Positive detections (PTP) 2
SIRV transcripts associated to PTP 126
False Negative (FN) 3
False Positive (FP) 160
Sensitivity 0.94
Precision 0.22
Non Redundant Precision 0.22
Positive Detection Rate 0.96
False Discovery Rate 0.44
False Detection Rate 0.44
Redundancy 2.53