prepUMI4C {UMI4Cats} | R Documentation

## Prepare UMI4C 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+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"
    )
    }

[Package UMI4Cats version 1.4.0 Index]