Running --> bedGraphToBigWig

[KEVIN KARIUKI WAMAE]

Hi, I downloaded the the above mentioned file form http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig.

I am running an online course on ChIP-Seq analysis and one of the steps requires that I use bedGraphToBigWig. So now I have the file, how do I run it?

Regards

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Kevin Kariuki W.
Centre For Biotechnology & Bioinformatics        
College of Biological and Physical Sciences                       
University of Nairobi

Kenya

website: http://cebib.uonbi.ac.ke/node/40

e-mail: kevin...@students.uonbi.ac.ke; wamae...@gmail.com

[Jonathan Casper]

Hello Kevin,

Thank you for your question about running the bedGraphToBigWig utility. The version of the program that you downloaded is for Linux x86_64 computers. As long as you are using one of those computers, you should be able to run the program just by typing bedGraphToBigWig on the command line while you are in the directory that contains the program. Note that on some systems, you may need to actually type "./bedGraphToBigWig" (without the quotes) for security reasons. Occasionally you may get a response that it is not an executable file or "Permission Denied". If so, you need to add the executable permission to the file. You can do that by running "chmod +x bedGraphToBigWig".

If you are using a recent Macintosh computer, you should instead download the program from the appropriate MacOSX directory at http://hgdownload.cse.ucsc.edu/admin/exe/. If you are using a Windows computer, you will need to explore your own options for downloading our source code (see the userApps.src.tgz file) and compiling it. We do not provide precompiled tools for Windows computers.

When you run the bedGraphToBigWig program alone without arguments, it displays the following usage message:

bedGraphToBigWig v 4 - Convert a bedGraph file to bigWig format.
usage:
   bedGraphToBigWig in.bedGraph chrom.sizes out.bw
where in.bedGraph is a four column file in the format:
      <chrom> <start> <end> <value>
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
The input bedGraph file must be sorted, use the unix sort command:
  sort -k1,1 -k2,2n unsorted.bedGraph > sorted.bedGraph
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.

More information on the bedGraph file format can be found at http://genome.ucsc.edu/goldenPath/help/bedgraph.html. The fetchChromSizes script can be found in the same directory where you downloaded the bedGraphToBigWig program.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

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