alignmentUMI4C: UMI4C alignment

In Pasquali-lab/UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

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")
)
}

Pasquali-lab/UMI4Cats documentation built on Nov. 3, 2024, 3:10 p.m.