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

This repository contains the source for the paper

Lobo AK, Traeger LL, Keller MP, Attie AD, Rey FE, Broman KW (2021) Identification of sample mix-ups and mixtures in microbiome data in Diversity Outbred mice. G3 (Bethesda) 11:jkab308

• mb_mixups.Rnw - Main text for the manuscript (LaTeX + R code, to be processed by knitr)
• 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
• here
• knitr
• data.table
• kableExtra
• magrittr

Additional data

• Intermediate data files at figshare doi:10.6084/m9.figshare.16413279

• Primary metagenomic sequence data at Sequence Read Archive (SRA), accession PRJNA744213

• SQLite database of variants in the Collaborative Cross founders at Figshare, doi:10.6084/m9.figshare.5280229.v3

License

This manuscript is licensed under CC BY.