October 2019
Intermediate to advanced
316 pages
9h 45m
English
Content preview from R Bioinformatics Cookbook
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How to do it...
Complete read-to-reference alignment with external programs using the following steps:
- Set up the files and executable paths:
bwa <- "/Users/macleand/miniconda2/bin/bwa"samtools <- "/Users/macleand/miniconda2/bin/samtools"reference <- file.path(getwd(), "datasets", "ch8", "ecoli_genome.fa")
- Prepare the index command and run:
command <- paste(bwa, "index", reference)system(command, wait = TRUE)
- Prepare the alignment command and run:
reads <- file.path(getwd(), "datasets", "ch8", "ERR019653.fastq.gz")output <- file.path(getwd(), "datasets", "ch8", "aln.bam")command <- paste(bwa, "mem", reference, reads, "|", samtools, "view -S -b >", output)system(command, wait = TRUE)
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