bowtie2_align: Bowtie2 Alignment

In Bankso/SCAR: SpLiT-ChEC analysis with R

Bowtie2 Alignment

Description

Bowtie2 Alignment

Usage

bowtie2_align(
  SCAR_obj,
  outdir = getwd(),
  alignment_mode = "end-to-end",
  min_fragment = NA,
  max_fragment = NA,
  mapq_val = 10,
  max_memory = "1G"
)

Arguments

SCAR_obj	SCAR object.
outdir	Output directory for aligned reads.
alignment_mode	Either 'end-to-end' or 'local'.
min_fragment	Minimum fragment length (paired end).
max_fragment	Maximum fragment length (paired end).
mapq_val	Minimum MAPQ value to accept reads. Used to filter via samtools post alignment
max_memory	Maximum memory per thread for samtools.

Bankso/SCAR documentation built on Aug. 20, 2022, 5:26 a.m.