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 5930
Number of known genes detected 5550
Number of transcripts detected 8631
Number of transcripts associated to a known gene 8149
Number of unique SJ detected 52579
Absolute value Relative value (%)
Novel SJ 970 0.02
Non-canonical SJ 0 0.00

Evaluation of FSM

Absolute value Relative value (%)
Number of isoforms 5649 -
Reference Match 3184 56.36
5’ reference supported (transcript) 4413 78.12
3’ reference supported (transcript) 4035 71.43
5’ reference supported (gene) 5160 91.34
3’ reference supported (gene) 5079 89.91
5’ CAGE supported 4544 80.44
3’ polyA supported 5609 99.29
Supported Reference Transcript Model (SRTM) 5379 95.22
Intra-priming 1 0.02
Reference redundancy Level 1 -

Evaluation of ISM

Absolute value Relative value (%)
Number of isoforms 399 -
5’ reference supported (transcript) 132 33.08
3’ reference supported (transcript) 194 48.62
5’ and 3’ reference supported (gene) 148 37.09
5’ reference supported (gene) 206 206
3’ reference supported (gene) 270 67.67
5’ CAGE supported 176 44.11
3’ polyA supported 345 86.47
Supported Reference Transcript Model (SRTM) 213 53.38
Intra-priming 1 0.25
Reference redundancy Level 1.02 -

Evaluation NIC

Absolute value Relative value (%)
Number of isoforms 1585 -
5’ and 3’ reference supported (gene) 1338 84.42
5’ reference supported (gene) 1464 92.37
3’ reference supported (gene) 1435 90.54
5’ CAGE supported 1378 86.94
3’ polyA supported 1566 98.8
Supported Novel Transcript Model (SNTM) 1394 87.95
Intra-priming 1 0.06
Intron retention incidence 515 32.49

Evaluation NNC

Absolute value Relative value (%)
Number of isoforms 516 -
5’ and 3’ reference supported (gene) 328 63.57
5’ reference supported (gene) 395 76.55
3’ reference supported (gene) 406 78.68
5’ CAGE supported 378 73.26
3’ polyA supported 508 98.45
Supported Novel Transcript Model (SNTM) 390 75.58
Non-canonical SJ incidence 0 0
Full Illumina SJ support 460 89.15
Intra-priming 1 0.19
RT-switching incidence 47 9.11

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) 74
SIRV transcripts associated to TP (Reference Match) 74
Partial True Positive detections (PTP) 2
SIRV transcripts associated to PTP 3
False Negative (FN) 8
False Positive (FP) 4
Sensitivity 0.88
Precision 0.91
Non Redundant Precision 0.91
Positive Detection Rate 0.9
False Discovery Rate 0.07
False Detection Rate 0.05
Redundancy 1.01