Getting ready...

We'll use base R only in this recipe, so you don't need to install any packages. You will need the reference genome FASTA file in datasets/ch8/ecoli_genome.fa and the datasets/ch8/ERR019653.fastq,gz file that we created in the Finding experiments and reads from SRA/ENA recipe. This recipe also requires a working copy of BWA and samtools on your system. The web pages for these pieces of software are at and If you have conda installed, you can install it with conda install -c bioconda bwa and conda install -c bioconda samtools

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