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
...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:
Current PDF of the paper at https://www.biostat.wisc.edu/~kbroman/publications/mb_mixups.pdf
This manuscript is licensed under CC BY.