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:

• R/qtl2
• R/qtl2fst
• fst
• R/broman
• R/lineup2
• R/mbmixture

Current PDF of the paper at https://www.biostat.wisc.edu/~kbroman/publications/mb_mixups.pdf

It's also on bioRxiv: https://doi.org/10.1101/529040

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License

This manuscript is licensed under CC BY.