ClIP_bw2: Build bigwigs

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Build bigwigs

Description

Build bigwigs

Usage

CLIP_bw2(
  sort_bam,
  res_dir = dirname(sort_bam),
  normalized = TRUE,
  stranded = FALSE,
  verbose = FALSE
)

Arguments

sort_bam	path to sorted BAM file.
res_dir	result directory, default is directory where BAM file is located, to specify other/create new directory, enter path as character string.
normalized	normalized to total reads.
stranded	Whether to make separate bigwigs for each strand, TRUE or FALSE (default).
verbose	print messages, TRUE or FALSE (default).

Value

bigwig.

Examples

testFasta <- system.file("extdata/hg19Small.fa",package="CLIPflexR")
myIndex <-suppressWarnings(bowtie2_index(testFasta, overwrite = TRUE))
testFQ <- system.file("extdata/Fox3_Std_small.fq.gz",package="CLIPflexR")
FqFile <- decompress(testFQ,overwrite = TRUE)
FqFile_FF <- ctk_fastqFilter(FqFile,qsFilter = "mean:0-29:20",verbose=TRUE)
FqFile_clipped <- fastx_clipper(FqFile_FF,length=20)
FqFile_QF <- fastq_quality_trimmer(FqFile_clipped)
FqFile_Col <- ctk_fastq2collapse(FqFile_QF,verbose = TRUE)
FqFile_ColStrip <- ctk_stripBarcode(FqFile_Col,linkerlength=5, inputFormat="fastq") 
##map reads to genome
mapped <- suppressWarnings(bowtie_align(FqFile_ColStrip,myIndex, 
mode="genome_map", inputFormat="fastq"))
wig <- CLIP_bw2(mapped)

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