.singleAlignmentUMI4C {UMI4Cats} | R Documentation

## Align split fastq file

### Description

Align split fastq file

### Usage

    .singleAlignmentUMI4C(
      split_file,
      align_dir,
      threads = 1,
      bowtie_index,
      pos_viewpoint,
      filter_bp = 1e+07
    )

### Arguments

`split_file` | Split fastq file to align.
`align_dir` | Directory where to save aligned files.
`threads` | Number of threads to use in the analysis. Default=1.
`bowtie_index` | Path and prefix of the bowtie index to use for the alignment.
`pos_viewpoint` | GRanges object containing the genomic position of the viewpoint.
`filter_bp` | Integer indicating the bp upstream and downstream of the viewpoint to select for further analysis. Default=10e6

### Value

Creates a BAM file in `wk_dir/align` named "`basename(fastq))_filtered.bam`", containing the aligned filtered reads. A data.frame object with the statisitics is also returned.

[Package UMI4Cats version 1.2.1 Index]