contactsUMI4C {UMI4Cats} | R Documentation

## UMI4C Contacts Processing

### Description

Using demultiplexed FastQ files as input, performs all necessary steps to end up with a tsv file summarizing the restriction enzyme fragments and the number of UMIs supporting that specific contact with the viewpoint (bait) of interest.

### Usage

    contactsUMI4C(
      fastq_dir,
      wk_dir,
      file_pattern = NULL,
      bait_seq,
      bait_pad,
      res_enz,
      cut_pos,
      digested_genome,
      bowtie_index,
      threads = 1,
      numb_reads = 1e+09,
      rm_tmp = TRUE,
      min_flen = 20,
      filter_bp = 1e+07,
      ref_gen,
      sel_seqname = NULL
    )

### 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.
`cut_pos` | Numeric indicating the nucleotide position where restriction enzyme cuts (zero-based) (for example, for DpnII is 0).
`digested_genome` | Path for the digested genome file generated using the `digestGenome` function.
`bowtie_index` | Path and prefix of the bowtie index to use for the alignment.
`threads` | Number of threads to use in the analysis. Default=1.
`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.
`rm_tmp` | Logical indicating whether to remove temporary files (sam and intermediate bams). TRUE or FALSE. Default=TRUE.
`min_flen` | Minimal fragment length to use for selecting the fragments. Default=20
`filter_bp` | Integer indicating the bp upstream and downstream of the viewpoint to select for further analysis. Default=10e6
`ref_gen` | A BSgenome object of the reference genome.
`sel_seqname` | A character with the chromosome name to focus the search for the viewpoint sequence.

### Value

This function is a combination of calls to other functions that perform the necessary steps for processing UMI-4C data.

### Examples

    if (interactive()) {
    path <- downloadUMI4CexampleData()

    hg19_dpnii <- digestGenome(
        cut_pos = 0,
        res_enz = "GATC",
        name_RE = "DpnII",
        ref_gen = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19,
        out_path = file.path(path, "digested_genome")
    )

    raw_dir <- file.path(path, "CIITA", "fastq")

    contactsUMI4C(
        fastq_dir = raw_dir,
        wk_dir = file.path(path, "CIITA"),
        bait_seq = "GGACAAGCTCCCTGCAACTCA",
        bait_pad = "GGACTTGCA",
        res_enz = "GATC",
        cut_pos = 0,
        digested_genome = hg19_dpnii,
        bowtie_index = file.path(path, "ref_genome", "ucsc.hg19.chr16"),
        threads = 1,
        numb_reads = 1e9,
        ref_gen = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19,
        sel_seqname = "chr16"
    )

    unlink(path, recursive=TRUE)
    }

[Package UMI4Cats version 1.4.0 Index]