ClIP_align: Align to Genome

CLIP_alignR Documentation

Align to Genome

Description

Align to Genome

Usage

CLIP_align(
  samID,
  res_dir = NULL,
  genome_idx = NULL,
  aligner = NULL,
  samSheet = NULL,
  thread = 4,
  bwa = NULL
)

Arguments

samID

sample id in the sample sheet.

res_dir

result directory.

genome_idx

path to indexed genome.

aligner

Assign aligner bowtie2/bwa_mem/bwa_alb/subread/subjunc/hisat2

samSheet

sample sheet.

thread

thread used in the processing, default is 4

bwa

executable bwa file path.

Value

path to sorted BAM file.

Examples

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

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