Prepare UMI4C data

Source: R/contactsUMI4C.R

Prepare the FastQ files for the further analysis by selecting reads with bait and adding the respective UMI identifier for each read in its header.

prepUMI4C(
  fastq_dir,
  wk_dir,
  file_pattern = NULL,
  bait_seq,
  bait_pad,
  res_enz,
  numb_reads = 1e+09
)

Arguments

fastq_dir

Path of the directory containing the FastQ files (compressed or uncompressed).
wk_dir

Working directory where to save the outputs generated by the UMI-4c analysis.
file_pattern

Character that can be used to filter the files you want to analyze in the fastq_dir.
bait_seq

Character containing the bait primer sequence.
bait_pad

Character containing the pad sequence (sequence between the bait primer and the restriction enzyme sequence).
res_enz

Character containing the restriction enzyme sequence.
numb_reads

Number of lines from the FastQ file to load in each loop. If having memory size problems, change it to a smaller number. Default=1e9.

Value

Creates a compressed FASTQ file in wk_dir/prep named basename(fastq)).fq.gz, containing the filtered reads with the UMI sequence in the header. A log file with the statistics is also generated in wk_dir/logs named umi4c_stats.txt.

See also

contactsUMI4C.

Examples

if (interactive()) {
path <- downloadUMI4CexampleData(reduced = TRUE)
raw_dir <- file.path(path, "CIITA", "fastq")

prepUMI4C(
    fastq_dir = raw_dir,
    wk_dir = file.path(path, "CIITA"),
    bait_seq = "GGACAAGCTCCCTGCAACTCA",
    bait_pad = "GGACTTGCA",
    res_enz = "GATC"
)
}