UMI4C alignment

Source: R/contactsUMI4C.R

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

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")
)
}