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What is the purpose of this block of code? Usually installation is handled separately from loading the packages. Were you able to get it to run?
I am closely following https://github.com/jdalapicolla/LanGen_pipeline_version2
But my data after the filter show no data left. Why? how do it make the script work?
Dear PhyloBio Team,
I am almost done with all analyses and pretty satisfied with the progress. Yet when I knit the markdown, it seems the visualization results differ every time? Why is it? I don't expect the result to change though because there is no random seed or permutations, etc...
Can you help? I don't know how to interpret the result now, because they seem to change every time. The colors should match the ancestry because I set the palette the same every time, didn't I?
From MVA document,
#Look at depth, quality, HWE, HE, allele frequencies, and Pi site.depth <- r2vcftools::Query(snps_unind, type="site-mean-depth") summary(site.depth$MEAN_DEPTH) #Mean = 3.59 / Median = 2, about 1/20 smaller than the example hist(site.depth$MEAN_DEPTH, breaks=200) quality <- Query(snps_unind, type="site-quality") summary(quality$QUAL) #all 13 with seemingly no variation hist(quality$QUAL) ## something wrong here.
I included in the output folder the Robject- "snps_unind", which should allow you to run the code from line 200.
Does it suggests anything wrong with my data quality?
Best,
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