makeJunctionTracksWrapper: Make Junction Tracks Wrapper

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

Description

A wrapper calls up three major functions to create junction bed file, junction tracks bigBed files, and generate a track line files specifying the attribute of the junciton track.

Usage

makeJunctionTracksWrapper(bamFiles, genome, cores = 1L,
                          seqlev = NULL, min_junction_count = 2,
			  bedDir = ".", juncDir = ".",
			  chrom_sizefile,
			  trackName)

Arguments

bamFiles	character strings of the bam files.
genome	a character string specifying the genome of the subject.
cores	an integer indicating the number of cores.
seqlev	character strings specifying the sequence levels desired to be included in the junction files.
min_junction_count	an integer specifying the minimal number of junction read.
bedDir	a character string indicating the destination of the junction bed (.bed) files.
juncDir	a character string indicating the destination of the junction bigBed (.bb) files. The preferred location is "/fh/fast/tapscott_s/pub/tapscott/ucsc/junctions/...".
chrom_sizefile	a file name of the chromozon size file pertained to the genome. Those files can be found in "/fh/fast/tapscott_s/CompBio/hg38, /mm10, and /canFam3".
trackName	a character string specifying the name of the track to be appeared on UCSC genome browser.

Details

The wrapper calls three functions: makeJunctionBed(), convertBedToBigBed(), and createHubTrackLine.junc.bed(). See example below.

Author(s)

Chao-Jen Wong <[e-mail]>

See Also

makeJunctionBed, createHubTrackLine.junc.bed

Examples

## Not run: 
pkgDir <- "/fh/fast/tapscott_s/R/RNA-Seq/canFam3.DuxFamily"
load(file.path(pkgDir, "data", "canine.ens.SE.rda"))
ucscDir <- "/fh/fast/tapscott_s/pub/tapscott/ucsc/junctions"
ngsDir <- "/shared/ngs/illumina/atyler/170208_SN367_0857_AHF37NBCXY"

## define parameters
bamDir <- file.path(ngsDir, "tophat", "bam")
bamFiles <- list.files(bamDir, pattern="\.bam$",
                       full.names=TRUE)[c(1,5, 6)]
seqlev <- seqlevels(canine.ens.SE)
chrom_sizefile <- "/fh/fast/tapscott_s/CompBio/canFam3/canFam3.chrom.sizes"
bedDir <- file.path(pkgDir, "inst", "junction_bed")
## bigBedDir is the location where files for the Hub reside.
bigBedDir <- file.path(ucscDir, "canFam3_CnMb_luciferase")
trackName <- "CnMb_luciferase_junc"

makeJunctionTracksWrapper(bamFiles, genome="canFam3",
                          cores=1L, seqlev=seqlev,
                          min_junction_count=2,
                          chrom_sizefile=chrom_sizefile,
                          bedDir=bedDir,
                          bigBedDir=bigBedDir,
                          trackName=trackName)

## End(Not run)

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