Darren's testing protocol
The various test files described can be downloaded from the “Example Datasets” tab in the user interface. The file links are organized relative to the figure in the paper which they contributed to, so you may have to look a bit to find the specific ones referenced below.
Where "different selections for bias corrections" is specified, the default bias corrections were applied for generating the associated cartoon, but it is also possible to play around with the bias corrections to make sure they work.
Note that some projects have dependencies as follows:
- 11 -> 10
- 12 -> 10
- 13 -> 10
- 14 -> 10
- 13 -> 8 -> 6 -> 4 -> 2
- 14 -> 9 -> 7 -> 4 -> 2
Dataset Name: test_SnpCghArray_Ss2
Ploidy of experiment: 2.0
Baseline ploidy: 2.0
Generate figure with annotations: Yes
Data type: SnpCgh microarray
[Different selections for bias corrections.]
Select "Add SnpCgh array data…” button and choose an array dataset. The specific dataset isn’t important for general testing.
Dataset Name: test_WGseq_SC5314
Ploidy of experiment: 2.0
Baseline ploidy: 2.0
Generate figure with annotations: Yes
Data type: Whole Genome NGS
Read type: "single-end reads” or "paired-end reads”
Reference genome: C_albicans_SC5314_vA21-s02-m09-r07
Haplotype map: [none defined]
Parental strain: [This strain is parental type]
[Different selections for bias corrections.]
Load one or two sequence files when prompted. These files should represent sequencing data from SC5314.
Dataset Name: test_WGseq_12353
Ploidy of experiment: 1.0
Baseline ploidy: 1.0
Generate figure with annotations: Yes
Data type: Whole Genome NGS
Read type: ["single-end reads” or "paired-end reads”]
Reference genome: C_albicans_SC5314_vA21-s02-m09-r07
Haplotype map: [none defined]
Parental strain: [This strain is parental type]
[Different selections for bias corrections.]
Load one or two sequence files when prompted. These files should represent sequencing data from haploid YJB12353.
Dependencies: [Project 2]
Dataset Name: test_WGseq_12353_vs_SC5314
Ploidy of experiment: 1.0
Baseline ploidy: 1.0
Generate figure with annotations: Yes
Data type: Whole Genome NGS
Read type: ["single-end reads” or "paired-end reads”]
Reference genome: C_albicans_SC5314_vA21-s02-m09-r07
Haplotype map: [none defined]
Parental strain: test_WGseq_SC5314
[Different selections for bias corrections.]
Load one or two sequence files when prompted. These files should represent sequencing data from haploid YJB12353.
Dataset Name: test_WGseq_12353_vs_SC5314Hapmap
Ploidy of experiment: 1.0
Baseline ploidy: 1.0
Generate figure with annotations: Yes
Data type: Whole Genome NGS
Read type: ["single-end reads” or "paired-end reads”]
Reference genome: C_albicans_SC5314_vA21-s02-m09-r07
Haplotype map: C_albicans_SC5314_A21-s02-m09-r07
[Different selections for bias corrections.]
Load one or two sequence files when prompted. These files should represent sequencing data from haploid YJB12353.
Dependencies: [Project 4][Project 2]
Hapmap Name: test_hapmap_1
Reference Diploid Genome: C_albicans_SC5314_vA21-s02-m-09-r07
Construct a hapmap from [one diploid] strains.
Parental strain: test_WGseq_SC5314
First strain: test_WGseq_12353_vs_SC5314
Define chr1 as all ‘a’.
Define chr2 as all ‘b’
Define first half of chrR as ‘a’.
Define second half of chrR as ‘b’
Select colors for each homolog in test_hapmap_1. Choose 'green' and 'dark orange' to match example outputs.
Select “Finalize haplotype map.” button once it appears.
Dependencies: [Project 4][Project 2]
Hapmap Name: test_hapmap_2
Reference Diploid Genome: C_albicans_SC5314_vA21-s02-m-09-r07
Construct a hapmap from [one diploid] strains.
Parental strain: test_WGseq_SC5314
First strain: test_WGseq_12353_vs_SC5314
Define chr1 as all ‘a’.
Define chr2 as all ‘b’.
Define chrR as half ‘a’ and half ‘b’.
Select colors you for each homolog in test_hapmap_2. Choose 'blue' and 'yellow' to match example outputs.
Select “Add haplotype entry...” button once it appears.
Next strain: test_WGseq_12353_vs_SC5314
Define chr3 as all ‘a’.
Define chr4 as all ‘b’.
Define first third of chr5 as ‘a’.
Define second third of chr5 as ‘b’.
Select “Finalize haplotype map.” button once it appears.
Dependencies: [Project 6][Project 4][Project 2]
Dataset Name: test_WGseq_12353_vs_hapmap_1
Ploidy of experiment: 1.0
Baseline ploidy: 1.0
Generate figure with annotations: Yes
Data type: Whole Genome NGS
Read type: ["single-end reads” or "paired-end reads”]
Reference genome: C_albicans_SC5314_vA21-s02-m09-r07
Haplotype map: test_hapmap_1
[Different selections for bias corrections.]
Load one or two sequence files when prompted. These files should represent sequencing data from haploid YJB12353.
Dependencies: [Project 7][Project 4][Project 2]
Dataset Name: test_WGseq_12353_vs_hapmap_2
Ploidy of experiment: 1.0
Baseline ploidy: 1.0
Generate figure with annotations: Yes
Data type: Whole Genome NGS
Read type: ["single-end reads” or "paired-end reads”]
Reference genome: C_albicans_SC5314_vA21-s02-m09-r07
Haplotype map: test_hapmap_2
[Different selections for bias corrections.]
Load one or two sequence files when prompted. These files should represent sequencing data from haploid YJB12353.
Dataset Name: test_ddRADseq_SC5314
Ploidy of experiment: 2.0
Baseline ploidy: 2.0
Generate figure with annotations: Yes
Data type: ddRADseq
Read type: TXT file
Reference genome: C_albicans_SC5314_vA21-s02-m09-r07
Haplotype map: [none defined]
Parental strain: [This strain is parental type]
[Different selections for bias corrections.]
Load ddRADseq TXT formatted data file for reference strain SC5314.
Dependencies: [Project 10]
Dataset Name: test_ddRADseq_11461_vs_SC5314
Ploidy of experiment: 2.0
Baseline ploidy: 2.0
Generate figure with annotations: Yes
Data type: ddRADseq
Read type: TXT file
Reference genome: C_albicans_SC5314_vA21-s02-m09-r07
Haplotype map: [none defined]
Parental strain: test_ddRADseq_SC5314
[Different selections for bias corrections.]
Load ddRADseq TXT formatted data file for strain YJB11461.
Dependencies: [Project 10]
Dataset Name: test_ddRADseq_11461_vs_SC5314_and_hapmap
Ploidy of experiment: 2.0
Baseline ploidy: 2.0
Generate figure with annotations: Yes
Data type: ddRADseq
Read type: TXT file
Reference genome: C_albicans_SC5314_vA21-s02-m09-r07
Haplotype map: C_albicans_SC5314_A21-s02-m09-r07
Parental strain: test_ddRADseq_SC5314
[Different selections for bias corrections.]
Load ddRADseq TXT formatted data file for strain YJB11461.
Dependencies: [Project 8][Project 6][Project 4][Project 2]; [Project 10]
Dataset Name: test_ddRADseq_11461_vs_SC5314_and_novelHapmap
Ploidy of experiment: 2.0
Baseline ploidy: 2.0
Generate figure with annotations: Yes
Data type: ddRADseq
Read type: TXT file
Reference genome: C_albicans_SC5314_vA21-s02-m09-r07
Haplotype map: test_hapmap1
Parental strain: test_ddRADseq_SC5314
[Different selections for bias corrections.]
Load ddRADseq TXT formatted data file for strain YJB11461.
Dependencies: [Project 9][Project 7][Project 4][Project 2]; [Project 10]
Dataset Name: test_ddRADseq_11461_vs_SC5314_and_novelHapmap
Ploidy of experiment: 2.0
Baseline ploidy: 2.0
Generate figure with annotations: Yes
Data type: ddRADseq
Read type: TXT file
Reference genome: C_albicans_SC5314_vA21-s02-m09-r07
Haplotype map: test_hapmap2
Parental strain: test_ddRADseq_SC5314
[Different selections for bias corrections.]
Load ddRADseq TXT formatted data file for strain YJB11461.
Dependencies: Any user-installed project and any system-installed project.
Confirm that both projects are displayed in the lower active-area and that both appear to have buttons available for all the different sub-figures associated with the project.