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4. Quality Control analysis
Use the excel to open the files The following files are going to be used for QC analysis: Merged.txt (raw variants data), haplocheck_results (contains the contamination status), andhaplogroups_workshopsamples.txt (contains the haplogroup information for each one of the samples).
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#NOTE: The homoplasmic_variants.txt file should be uploaded into your folder (directory) in the SCC cluster.
#NOTE: Save the
Homoplasmy and heteroplasmy – transition and transversion rates.
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- Copy the entire data from the homoplasmy_only tab (from MergeMerged.csv txt file) and paste it into a new excel file. Next, follow the steps described below:
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