prepUMI4C: Prepare UMI4C data

In UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

Description

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.

Usage

prepUMI4C(
  fastq_dir,
  wk_dir,
  file_pattern = NULL,
  bait_seq,
  bait_pad,
  res_enz,
  numb_reads = 1e+11
)

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=10e10.

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"
)
}

UMI4Cats documentation built on Dec. 31, 2020, 2:01 a.m.