CLIP_buildIDX: Build index for reference genome

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Build index for reference genome

Description

Build index for reference genome

Usage

CLIP_buildIDX(
  ref_seq = NULL,
  res_dir = NULL,
  preFIX = NULL,
  aligner = NULL,
  thread = 4,
  bwa = NULL
)

Arguments

ref_seq	path to reference genome.
res_dir	result directory.
preFIX	file name prefix for indexed genome.
aligner	Assign aligner bowtie2/subread/bwa/hisat2.
thread	threads used in processing, default is 4.
bwa	executable bwa file path.

Value

indexed reference genome.

Examples

testFQ <- system.file("extdata/Fox3_Std_small.fq.gz",package="CLIPflexR")

kathrynrozengagnon/CLIPflexR documentation built on Dec. 8, 2022, 7:31 p.m.