Build index for reference genome — CLIP_buildIDX • CLIPflexR

Build index for reference genome

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")