Last updated: 2022-11-09

Checks: 1 1

Knit directory: MUGA_reference_data/

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Repository version: 1074529

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Ignored files:
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Untracked files:
    Untracked:  README.html
    Untracked:  data/GigaMUGA/FPGM_1-6_FinalReport.txt
    Untracked:  data/GigaMUGA/FPGM_1-6_FinalReport.zip
    Untracked:  data/GigaMUGA/GigaMUGA_control_genotypes.txt
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    Untracked:  data/GigaMUGA/GigaMUGA_reference_genotypes/
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Unstaged changes:
    Modified:   analysis/GigaMUGA_Reference_QC.Rmd
    Modified:   analysis/MUGA_Reference_QC.Rmd
    Modified:   analysis/MegaMUGA_Reference_QC.Rmd
    Modified:   analysis/_site.yml
    Modified:   analysis/index.Rmd
    Deleted:    code/GigaMUGA_Reference_QC.Rmd
    Deleted:    code/GigaMUGA_Reference_QC.html
    Deleted:    code/MUGA_Reference_QC.Rmd
    Deleted:    code/MUGA_Reference_QC.html
    Deleted:    code/MegaMUGA_Reference_QC.Rmd
    Deleted:    code/MegaMUGA_Reference_QC.html
    Modified:   data/GigaMUGA/GigaMUGA_BadSamples_BadMarkers.RData
    Modified:   data/GigaMUGA/GigaMUGA_QC_Results.RData
    Modified:   data/GigaMUGA/GigaMUGA_SexCheck_Results.RData
    Modified:   data/GigaMUGA/gm_uwisc_v2.csv

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File Version Author Date Message
Rmd 1074529 sam-widmayer 2022-11-08 update markdown formatting for workflowr
Rmd 54f4404 sam-widmayer 2022-11-08 Start workflowr project.

MUGA Genotype Data for Reference Samples and CC/DO Founder Strains

File Name Description Link
MUGA_sample_metadata.csv Metadata for samples passing QC from reference strains (sample name, sex, strain) [TBD]
MUGA_founder_metadata.csv Metadata for CC/DO founder strain samples passing QC (sample name, sex, strain, letter code) [TBD]
MUGA_genotypes.csv.gz Genotypes for markers passing QC from reference samples [TBD]
MUGA_x_intensities.csv.gz Probe x-channel intensities from markers passing QC from reference samples [TBD]
MUGA_y_intensities.csv.gz Probe y-channel intensities from markers passing QC from reference samples [TBD]
MUGA_founder_consensus_genotypes.csv.gz CC/DO founder strain consensus genotypes for markers passing QC [TBD]
MUGA_founder_mean_x_intensities.csv.gz CC/DO founder strain-averaged probe intensities (x-channel) for all markers passing QC [TBD]
MUGA_founder_mean_y_intensities.csv.gz CC/DO founder strain-averaged probe intensities (y-channel) for all markers passing QC [TBD]

MegaMUGA Genotype Data for Reference Samples and CC/DO Founder Strains

File Name Description Link
MegaMUGA_sample_metadata.csv Metadata for samples passing QC from reference strains (sample name, sex, strain) [TBD]
MegaMUGA_founder_metadata.csv Metadata for CC/DO founder strain samples passing QC (sample name, sex, strain, letter code) [TBD]
MegaMUGA_genotypes.csv.gz Genotypes for markers passing QC from reference samples [TBD]
MegaMUGA_x_intensities.csv.gz Probe x-channel intensities from markers passing QC from reference samples [TBD]
MegaMUGA_y_intensities.csv.gz Probe y-channel intensities from markers passing QC from reference samples [TBD]
MegaMUGA_founder_consensus_genotypes.csv.gz CC/DO founder strain consensus genotypes for markers passing QC [TBD]
MegaMUGA_founder_mean_x_intensities.csv.gz CC/DO founder strain-averaged probe intensities (x-channel) for all markers passing QC [TBD]
MegaMUGA_founder_mean_y_intensities.csv.gz CC/DO founder strain-averaged probe intensities (y-channel) for all markers passing QC [TBD]

GigaMUGA Genotype Data for Reference Samples and CC/DO Founder Strains

File Name Description Link
GigaMUGA_sample_metadata.csv Metadata for samples passing QC from reference strains (sample name, sex, strain) [TBD]
GigaMUGA_founder_metadata.csv Metadata for CC/DO founder strain samples passing QC (sample name, sex, strain, letter code) [TBD]
GigaMUGA_genotypes.csv.gz Genotypes for markers passing QC from reference samples [TBD]
GigaMUGA_x_intensities.csv.gz Probe x-channel intensities from markers passing QC from reference samples [TBD]
GigaMUGA_y_intensities.csv.gz Probe y-channel intensities from markers passing QC from reference samples [TBD]
GigaMUGA_founder_consensus_genotypes.csv.gz CC/DO founder strain consensus genotypes for markers passing QC [TBD]
GigaMUGA_founder_mean_x_intensities.csv.gz CC/DO founder strain-averaged probe intensities (x-channel) for all markers passing QC [TBD]
GigaMUGA_founder_mean_y_intensities.csv.gz CC/DO founder strain-averaged probe intensities (y-channel) for all markers passing QC [TBD]