In uashogeschoolutrecht/structural_colours: Package For Project Structural Colour

knitr::opts_chunk$set(echo = TRUE)

file = readLines(con = "/home/rstudio/scpackage/inst/extdata/ERR833272_2.fastq")

# creating subset for testing
#counter = 0
#test_file = ""
#for (line in file) {
#  if (counter < 8) {
#    test_file = append(test_file, line)
#  }
#  counter = counter + 1
#}
#test_file = test_file[-1]

#checking quality distribution and range
all_qual = concatenate_fastq_qualities(file)
boxplot(gtools::asc(all_qual, simplify = TRUE))
ASCII_range_concatenated_qualities(all_qual)

#to go from +39 to +33, -6 ascii chars
rescale_phred_score(file_lines = file, scale_metric = -6, outfile = "/home/rstudio/scpackage/inst/ERR833272_2_rescaled_test.fastq")

uashogeschoolutrecht/structural_colours documentation built on June 20, 2020, 4:07 p.m.