splitUMI4C {UMI4Cats} | R Documentation

## Split UMI4C reads

### Description

Split the prepared reads using the restrition enzyme information.

### Usage

    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
    )
    }

[Package UMI4Cats version 1.2.1 Index]