dot-singleAlignmentUMI4C: Align split fastq file

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

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.

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