makeJunctionTracksWrapper <- function(bamFiles, genome,
cores=1L,
seqlev=NULL,
min_junction_count=2,
bedDir=".",
juncDir=".",
chrom_sizefile,
trackName) {
## this wrapper makes bed12 files for junction and convert bed files
## to bigBed files for UCSC genome brower
## the main directory of juncDir should be
## "/fh/fast/tapscott_s/pub/tapscott/ucsc/junctions"
#' (1) santity check
bdFiles <- makeJunctionBed(bamFiles=bamFiles, cores=cores, seqlev=seqlev,
min_junction_count=min_junction_count,
genome=genome, verbose=TRUE,
ignore.strand=TRUE, outdir=bedDir)
convertBedToBigBed(bedFiles, sample_name=NULL, cores=cores,
chrom_sizefile, outdir=juncDir)
createHubTrackLine.junc.bed(bbDir=juncDir,
trackName=trackName,
pattern="\\.bb$")
}
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