bedUniformLength

A genomics tool to make all regions in a bed file the same length. The noGap.bed file is used to ensure that regions are not extended into assembly gaps. I often use this tool when you have a set of regions, often of different lengths, but you want to apply a function to them that needs a fixed region size. For example: you want to predict enhancers and your prediction method is set to learn based on 1kb windows. You now need to get a set of posible training examples, known enhancers, and make them all 1kb in length.

Installation

This code uses the Kent libraries from UCSC so that must be installed to compile bedUniformLength

1. Download and compile the Kent Libraries
   1. Check the setting of your machtype variable with:
      echo $MACHTYPE
      it should be something in this list: i386 i686 sparc alpha x86_64 ppc. If it is not, set your machtype variable.
   2. Go to a folder on your computer where you want the kent source tree to reside and type:
      git clone git://genome-source.cse.ucsc.edu/kent.git
      to download the repository onto your own computer.
   3. go to the src/lib directory within the kent source repo that you just cloned:
      cd kent/src/lib
      
   4. Compile the libraries
      make
   5. If this was successful, you should have a file here:
      kent/src/lib/x86_64/jkweb.a
      the x86_64 will be the machtype of your machine.
      

   If this was not successful then you should look at the build instructions in the kent repo itself by looking at this file:
   kent/src/product/README.building.source

2. Compile bedUniformLength
   1. Edit the bedUniformLength makefile so that it points to the kent libraries on your system. These are the two lines you will have to modify:
      HG_INC += -I/home/lowec/kent/src/hg/inc -I/home/lowec/kent/src/inc
      L += /home/lowec/kent/src/lib/${MACHTYPE}/jkweb.a
      
   2. Compile bedUniformLength:
      make
   3. Running bedUniformLength with no parameters should give a brief help message.

References

This code has not yet been described in a publication.