bedgraphToBigWig: Bedgraph files to bigwig format

In e-myers/rnaseq: Process, Analyze and Visualize RNA-seq Data

Description

Take a list of bedgraph files and write a bigwig file for each one.

Usage

bedgraphToBigWig(filenames, genomeSizeFile, ucscPath = "/opt/UCSCtools/",
  outDest = "./", outSuffix = "")

Arguments

filenames	Character - List of bedgraph files
genomeSizeFile	String - Filename (with path) to text file containing genome size information
ucscPath	String - Path to UCSC tools executables
outDest	String - Directory where bigwig files should be written
outSuffix	String - will be appended to original filename (and ".bedgraph" is replaced by ".bigwig")

Details

Use UCSC function bedgraphToBigWig to convert bedgraph files to bigwig format. Requires UCSC tools to be installed. Time: ~40s - 1m per bedgraph, where the bedgraphs are generally ~400-800 MB. Example at the command line: system2('/opt/UCSCtools/wigToBigWig', args=c('samplename.gencov.bedgraph', '/path/to/genomeSizeFile.txt', samplename.bigwig))

Author(s)

Emma Myers

Examples

bedgraphToBigWig(filenames, genomeSizeFile="/path/to/genomeSizeFile.txt")

e-myers/rnaseq documentation built on May 20, 2019, 9:14 p.m.