7.3 Mapping aligned reads to the genome (also with QuasR)

library(QuasR)

# copy example data to current working directory
file.copy(system.file(package="QuasR", "extdata"), ".", recursive=TRUE)

# genome file in fasta format
genomeFile <- "extdata/hg19sub.fa"

# text file containing sample names and fastq file paths
sampleFile <- "extdata/samples_chip_single.txt"

# create alignments 
proj <- qAlign(sampleFile, genomeFile)