.singleCounterUMI4C {UMI4Cats} | R Documentation

## Count UMIs for a given bam file.

### Description

Count UMIs for a given bam file.

### Usage

    .singleCounterUMI4C(
      filtered_bam_R1,
      filtered_bam_R2,
      digested_genome_gr,
      pos_viewpoint,
      res_enz,
      count_dir,
      filter_bp = 1e+07
    )

### Arguments

`filtered_bam_R1` | R1 bam file.
`filtered_bam_R2` | R2 bam file.
`digested_genome_gr` | GRanges object containing the coordinates for the digested genome.
`pos_viewpoint` | Vector consist of chromosome, start and end position of the viewpoint.
`res_enz` | Character containing the restriction enzyme sequence.
`count_dir` | Counter directory.
`filter_bp` | Integer indicating the bp upstream and downstream of the viewpoint to select for further analysis. Default=10e6

### Value

Creates a tab-delimited file in `wk_dir/count` named "`basename(fastq) _counts.tsv`", containing the coordinates for the viewpoint fragment, contact fragment and the number of UMIs detected in the ligation.

[Package UMI4Cats version 1.2.1 Index]