Build bigwigs
CLIP_bw2(
sort_bam,
res_dir = dirname(sort_bam),
normalized = TRUE,
stranded = FALSE,
verbose = FALSE
)path to sorted BAM file.
result directory, default is directory where BAM file is located, to specify other/create new directory, enter path as character string.
normalized to total reads.
Whether to make separate bigwigs for each strand, TRUE or FALSE (default).
print messages, TRUE or FALSE (default).
bigwig.
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)
#> fastq_filter.pl command is /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq_filter.pl
#> fastq_filter.pl arguments are /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq_filter.pl -if sanger -of fastq -f mean:0-29:20 /Users/runner/work/_temp/Library/CLIPflexR/extdata/Fox3_Std_small.fq /Users/runner/work/_temp/Library/CLIPflexR/extdata/FF_Fox3_Std_small.fq
FqFile_clipped <- fastx_clipper(FqFile_FF,length=20)
FqFile_QF <- fastq_quality_trimmer(FqFile_clipped)
FqFile_Col <- ctk_fastq2collapse(FqFile_QF,verbose = TRUE)
#> fastq_filter.pl command is /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq2collapse.pl
#> fastq_filter.pl arguments are /Users/runner/Library/r-miniconda/envs/CLIPflexR_0.1.20/bin/ctk/fastq2collapse.pl /Users/runner/work/_temp/Library/CLIPflexR/extdata/QT_FF_Fox3_Std_small_clip.fq /Users/runner/work/_temp/Library/CLIPflexR/extdata/Collapsed_QT_FF_Fox3_Std_small_clip.fq
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)