Wiggle-Tools

Collection of scripts for generating BigWig files.

• GCcontent2bigwig.py: calculate GC content from a FASTA file and convert it to BigWig file format.

• gap2bigwig.py: find out gap regions (i.e., N base) from a FASTA file and convert to a BigWig file format.

Usage

• GCcontent2bigwig.py:

    GCcontent2bigwig.py <FASTA file>
    [-o, --bigwig_filename=<output file name>
    -t, --tempfile
    -k, --keep_tempfile
    -g, --gzip]

• gap2bigwig.py:

    gap2bigwig.py <FASTA file>
    [-o, --bigwig_filename=<output file name>
     -t, --tempfile
     -k, --keep_tempfile
     -g, --gzip]

Prerequsites

• Linux - tested on CentOS 6 x86_64 (should work on Mac, may work on windows if you can compile wigToBigWig by yourself)
• Python 2.7

Installation

• wigToBigWig
  • Download binary:
    • linux: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/wigToBigWig
    • mac: http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.x86_64/wigToBigWig
  • Make wigToBigwig executable: chmod +x wigToBigWig
  • Put in your $PATH, for example, most user have /usr/local/bin in $PATH, so just copy the binary into it: cp wigToBigWig /usr/local/bin