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 15288
Number of known genes detected 15211
Number of transcripts detected 45980
Number of transcripts associated to a known gene 45571
Number of unique SJ detected 166127
Absolute value Relative value (%)
Novel SJ 4863 0.03
Non-canonical SJ 589 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 33471 -
Reference Match 32932 98.39
5’ reference supported (transcript) 33144 99.02
3’ reference supported (transcript) 33126 98.97
5’ reference supported (gene) 33320 99.55
3’ reference supported (gene) 33273 99.41
5’ CAGE supported 24506 73.22
3’ polyA supported 28547 85.29
Supported Reference Transcript Model (SRTM) 33277 99.42
Intra-priming 787 2.35
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 1324 -
5’ reference supported (transcript) 615 46.45
3’ reference supported (transcript) 291 21.98
5’ and 3’ reference supported (gene) 410 30.97
5’ reference supported (gene) 895 895
3’ reference supported (gene) 649 49.02
5’ CAGE supported 626 47.28
3’ polyA supported 1186 89.58
Supported Reference Transcript Model (SRTM) 881 66.54
Intra-priming 61 4.61
Reference redundancy Level 1.16 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 7618 -
5’ and 3’ reference supported (gene) 4917 64.54
5’ reference supported (gene) 5817 76.36
3’ reference supported (gene) 6383 83.79
5’ CAGE supported 3768 49.46
3’ polyA supported 7551 99.12
Supported Novel Transcript Model (SNTM) 5628 73.88
Intra-priming 55 0.72
Intron retention incidence 2114 27.75

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 3158 -
5’ and 3’ reference supported (gene) 1353 42.84
5’ reference supported (gene) 1924 60.92
3’ reference supported (gene) 2201 69.7
5’ CAGE supported 1414 44.78
3’ polyA supported 3100 98.16
Supported Novel Transcript Model (SNTM) 1544 48.89
Non-canonical SJ incidence 515 16.31
Full Illumina SJ support 2352 74.48
Intra-priming 27 0.85
RT-switching incidence 283 8.96

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 81
True Positive detections (TP) 81
SIRV transcripts associated to TP (Reference Match) 81
Partial True Positive detections (PTP) 0
SIRV transcripts associated to PTP 0
False Negative (FN) 3
False Positive (FP) 0
Sensitivity 0.96
Precision 1
Non Redundant Precision 1
Positive Detection Rate 0.96
False Discovery Rate 0
False Detection Rate 0
Redundancy 1