Split UMI4C reads

Source: R/contactsUMI4C.R

Split the prepared reads using the restrition enzyme information.

splitUMI4C(wk_dir, res_enz, cut_pos, numb_reads = 1e+09, min_flen = 20)

Arguments

wk_dir

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

Character containing the restriction enzyme sequence.
cut_pos

Numeric indicating the nucleotide position where restriction enzyme cuts (zero-based) (for example, for DpnII is 0).
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.
min_flen

Minimal fragment length to use for selecting the fragments. Default=20

Value

Creates a compressed FASTQ file in wk_dir/split named basename(fastq)).fq.gz, containing the split reads based on the restriction enzyme used.

Examples

if (interactive()) {
path <- downloadUMI4CexampleData(reduced = TRUE)

splitUMI4C(
    wk_dir = file.path(path, "CIITA"),
    res_enz = "GATC",
    cut_pos = 0
)
}