GitHub - kbroman/Paper_MBmixups: Source files for a paper about identifiying sample mix-ups and mixtures in microbiome data

Identification of sample mix-ups and mixtures in microbiome data in Diversity Outbred mice

Files for a paper (in preparation) on detecting sample mix-ups and mixtures in microbiome data in Diversity Outbred mice.

mb_mixups.Rnw - Make text for the manuscript
mb_mixups.bib - BibTeX file with bibliography
Analysis/ - directory contain basic analyses and summarized results; the raw data and pipeline to get data summaries are elsewhere
Data/ - summarized data sets for the analysis
R/ - Code for making the figures (plus the basic analyses)

The initial work involved:

mapping sequence reads to the mouse genome using bowtie
generating pileup files using tools + Rsamtools (code BamFile(), ScanBamParam(), pileup())
...look for reads that overlap each possible SNP among the 8 founder lines and get counts of reads for each of the two alleles
separately, use calculated genotype probabilities + SNP database on founders to get inferred genotypes at all SNPs for all DO offspring

R packages needed to compile the paper:

This manuscript is licensed under CC BY.

Type	Name	Latest commit message	Commit time
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	Analysis
	Data
	R
	.gitignore
	LICENSE.md
	Makefile
	ReadMe.md
	genetics.bst
	mb_mixups.Rnw
	mb_mixups.bib