genomeCoverageBed: BAM or bed files to bedgraph with histogram of coverage...
In e-myers/rnaseq: Process, Analyze and Visualize RNA-seq Data

Description Usage Arguments Details Author(s) Examples

For each specified bed or bam file, apply the bedtools genomeCoverageBed function to get a bedgraph file with histogram of coverage values.

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genomeCoverageBed(filenames, genomeSizeFile,
  bedtoolsPath = "/opt/bedtools2/bin/", samtoolsPath = "~/anaconda2/bin/",
  outDest = "./", outSuffix = "", norm = FALSE, strand = NULL)

`filenames`	Character - List of BAM files
`genomeSizeFile`	String - Filename (with path) to text file containing genome size information
`bedtoolsPath`	String - Path to bedtools executables
`samtoolsPath`	String - Path to samtools exectuables
`outDest`	String - Directory where bedgraph files should be written
`outSuffix`	String - will be appended to original filename
`norm`	Logical - whether to normalize read counts to RPM (requires BAM input)
`strand`	String - For paired-end data; only do forward- or only do reverse-strand reads ("+" or "-"): "plus" or "minus" will be appended to filename

For each specified bed or bam file, apply the bedtools genomeCoverageBed function to get a bedgraph file with histogram of coverage values. Requires bedtools and samtools to be installed. Requires tools package. Note that it's a bit faster with bed than bam input files. But if you do "norm", you have to give it a BAM file, not a bed file. TIME: ~2.5m for 600 MB bam file; ~4m for an 815 MB bam file. Slightly shorter starting from bed file (2 and 3m). IMPROVE: Make it time calculating scaling factors too. And give total time for each file and for all files. Command line examples: $ /opt/bedtools2/bin/genomeCoverageBed -g /path/to/genome_size.tab.txt -i samplename.bed -bg -split > samplename.gencov.bedgraph Or, for bam input: $ /opt/bedtools2/bin/genomeCoverageBed -g /path/to/genome_size.tab.txt -ibam samplename.bam -bg -split > samplename.gencov.bedgraph To normalize by reads per million: $ uniqueReads=$(samtools view -F 0x904 -c samplename.bam) # those flags in the samtools view command get the number of uniquely mapped reads in BAM $ /opt/bedtools2/bin/genomeCoverageBed -g /path/to/genome_size.tab.txt -ibam samplename.bam -bg -scale 1000000/uniqueReads > samplename.gencov.bedgraph

Emma Myers