Align split fastq file

Source: R/contactsUMI4C.R

Align split fastq file

.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.