Align to Genome — CLIP_align • CLIPflexR

Align to Genome

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")