Usage: makeUCSCfile <tag directory> [options]

	Creates a bedgraph file for visualization using the UCSC Genome Browser

	General Options:
		-fsize <#> (Size of file, when gzipped, default: 5e7)
		-strand <both|separate|+|-> (control if reads are separated by strand, default: both)
		-fragLength <# | auto | given> (Approximate fragment length, default: auto)
		-adjust <#> (Adjust edge of tag 3' by # bp, negative for 5', default: none[good for dnase])
		-tbp <#> (Maximum tags per bp to count, default: no limit)
		-mintbp <#> (Minimum tags per bp to count, default: no limit)
		-res <#> (Resolution, in bp, of file, default: 1)
			-avg (report average coverage if resolution is larger than 1bp, default: max is reported)
		-lastTag (To keep ucsc happy, last mapped tag is NOT extended by default
			Using this option will allow extending of data past the last tag position)
		-norm <#> (Total number of tags to normalize experiment to, default: 1e7)
		-normLength <#> (Expected length of fragment to normalize to [0=off], default: 100)
		-noadj (Do not normalize tag counts)
		-neg (plot negative values, i.e. for - strand transcription)
		-CpG (Show unmethylated CpG ratios)
		-color <(0-255),(0-255),(0-255)> (no spaces, rgb color for UCSC track, default: random)
		-i <input tag directory> (normalize bedGraph to input data)
			-pseudo <#> (Number of pseudo counts used to smooth out low coverage areas, default: 5)
			-log (report log2 ratio instead of linear ratio)
			-inputtbp <#>, -inputFragLength <#>, -inputAdjust <#> can also be set
		-bigWig <chrom.size file> (creates a full resolution bigWig file and track line file)
			This requires bedGraphToBigWig to be available in your executable path
			Also, because how how bigWig files work, use "-strand -" and "-strand +"
			in separate runs to make strand specific files: "-strand separate" will not work
			Consider using makeBigWig.pl and makeMultiWigHub.pl if interested in bigWigs
		-o <filename|auto> (send output to this file - will be gzipped, default: prints to stdout)
			auto: this will place an appropriately named file in the tag directory
		-name <...> (Name of UCSC track, default: auto generated)
		-style <option> (See options below:)
			chipseq (standard, default)
			rnaseq (strand specific, if unstranded add '-strand both' to end of command)
			tss (strand specific, single bp fragment length)
			dnase (fragments centered on tag position instead of downstream)
			methylated (single bp resolution of cytosine methylation)
			unmethylated (single bp resolution of unmethylated cytosines)
			damid (2kb fragments centered on 5' end of reads)
		-circos <chrN:XXX-YYY|genome> (output only a specific region for circos[no header])