alignmentUMI4C {UMI4Cats} | R Documentation

## UMI4C alignment

### Description

Align split UMI-4C reads to a reference genome using Bowtie2.

### Usage

    alignmentUMI4C(
      wk_dir,
      pos_viewpoint,
      bowtie_index,
      threads = 1,
      filter_bp = 1e+07
    )

### Arguments

`wk_dir` | Working directory where to save the outputs generated by the UMI-4c analysis.
`pos_viewpoint` | GRanges object containing the genomic position of the viewpoint. It can be generated by `getViewpointCoordinates` 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.
`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. The alignment log is also generated in `wk_dir/logs` named "`umi4c_alignment_stats.txt`".

### Examples

    if (interactive()){
    path <- downloadUMI4CexampleData(reduced = TRUE)
    alignmentUMI4C(
        wk_dir = file.path(path, "CIITA"),
        pos_viewpoint = GenomicRanges::GRanges("chr16:10972515-10972548"),
        bowtie_index = file.path(path, "ref_genome", "ucsc.hg19.chr16")
    )
    }

[Package UMI4Cats version 1.0.1 Index]