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Samples were cleaned with Agencourt AMPure XP magnetic beads and adapter (Beckman Coulter, Indianapolis, IN) and quantified for amplicons with Qubit fluorometer (Thermo Fischer Scientific, Carlsbad, CA). Samples were pooled to 1 ng of DNA per sample, and sent in for sequencing on an Illumina MiSeq (Illumina, San Diego, CA) at the UC Davis Genome Center Sequencing Core.  Sequences were demultiplexed using a custom in-house script (https://github.com/gjospin/scripts/blob/master/Demul_trim_prep.pl), which automates quality assessment and trimming. Fasta files were then analyzed using a standard QIIME \cite{Caporaso_2010} workflow for analyzing microbial community data (http://www.wernerlab.org/teaching/qiime/overview). Figures were produced in R version 3.2.2 using the phyloseq \cite{McMURDIE_2011} package. We used unweighted UniFrac \cite{Lozupone_2005} to produce the figures for our data, and QIIME to calculate statistics on alpha and beta diversity data (p values (p-values  less than 0.05 were considered significant).