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bedGraphToBigWig

Reference Code backup Executable files

Convert a bedGraph file to bigWig format.

Category

Format Conversion

Usage

bedGraphToBigWig in.bedGraph chrom.sizes out.bw

Manual

This tool is part of UCSC Genome Browser's utilities.

Parameters

  • in.bedGraph: a four column file in the format: <chrom> <start> <end> <value> (columns are separated by Tab).
  • chrom.sizes: a two column file/URL: <chromosome name> <size in bases> (columns are separated by Tab)
  • out.bw: the output indexed bigwig file.

Options

  • -blockSize=N: Number of items to bundle in r-tree. Default 256
  • -itemsPerSlot=N: Number of data points bundled at lowest level. Default 1024
  • -unc: If set, do not use compression.

If the assembly is hosted by UCSC, chrom.sizes can be a URL like http://hgdownload.soe.ucsc.edu/goldenPath//bigZips/.chrom.sizes or you may use the script fetchChromSizes to download the chrom.sizes file. If not hosted by UCSC, a chrom.sizes file can be generated by running twoBitInfo on the assembly .2bit file.

The input bedGraph file must be sorted, use the unix sort command:

sort -k1,1 -k2,2n unsorted.bedGraph > sorted.bedGraph

Protocols using this tool

ENCODE RNA-seq (paired-end)

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