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
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mb_mixups.Rnw
- Main text for the manuscript (LaTeX + R code, to be processed by knitr)mb_mixups.bib
- BibTeX file with bibliographyAnalysis/
- directory contain basic analyses and summarized results; the raw data and pipeline to get data summaries are elsewhereData/
- summarized data sets for the analysisR/
- Code for making the figures (plus the basic analyses)
The initial work involved:
-
mapping sequence reads to the mouse genome using bowtie
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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
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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:
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Intermediate data files at figshare doi:10.6084/m9.figshare.16413279
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Primary metagenomic sequence data at Sequence Read Archive (SRA), accession PRJNA744213
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SQLite database of variants in the Collaborative Cross founders at Figshare, doi:10.6084/m9.figshare.5280229.v3
This manuscript is licensed under CC BY.