makeJunctionBed: Make Junction Bed Files from BAM files

In TapscottLab/UCSCTrackTools: Tools to convert BAM files to BigWig and to create session track line

Description

Calculate juntions from BAMs files

Usage

makeJunctionBed(bamFiles, cores = 1, seqlev = NULL, genome = NULL,
                verbose = TRUE, ignore.strand = TRUE, outdir = ".")

Arguments

bamFiles	A character vector identifying BAM files that are used to find junctions.
cores	An integer indicating number of cores available for parallel processing.
seqlev	A character vector indicating the chromosome of interest.
genome	A character string identifying a genome, usually one assiagned by UCSC, like "mm10".
verbose	If "TRUE", generate message indicating progress.
ignore.strand	Logical indicating whether to ignore strand. At this moment, it is set to "TRUE" internally.
outdir	A string indicating the output directory.

Details

This function imports reads from BAM files and the method to calculate junction coutns is adapted from the SGSeq packages.

Author(s)

Chao-Jen Wong <[e-mail]>

See Also

createHubTrackLine.junc.bed

Examples

 ## Not run: 
bam_file <- "/shared/ngs/illumina/jwhiddon/150918_SN367_0553_AH7YLFBCXX/tophat/bam/C2C12_mDuxCA_36h_15B_DOX1.bam"
seqlev <- paste0("chr", c(1:19, "M", "X", "Y"))
makeJunctionBed(bamFiles=bam_file, cores=4, seqlev=seqlev,
                genome="mm10",
                ignore.strand=TRUE, verbose=TRUE)
		
## if you want to view from UCSC Hub track (not session), you need to convert
## the bed file to bigBed format 
size_file <- "/fh/fast/tapscott_s/CompBio/mm10/mm10.chrom.sizes"
bedDir <- "/fh/fast/tapscott_s/CompBio/RNA-Seq/mm10.C2C12.mDux/inst/bed"
UCSCTrackTools:::convertBedToBigBed(file.path(bedDir,
                                              "C2C12_mDuxCA_36h_15B_DOX1.bed"),
                                    chrom_sizefile=size_file,
				    cores=1)
## make hub trackline for bigBed or bed (15) files

 
## End(Not run)

TapscottLab/UCSCTrackTools documentation built on May 16, 2019, 2:28 a.m.