Home
**bwtool** is a command-line utility for bigWig files. bigWigs are an indexed and compressed form of wig file, a somewhat standard format for storing genome-wide real-valued signal data. Much of the ENCODE processed data is in this form, and it is appearing more often in GEO as well. The purpose of bwtool is to make these files more useful by providing some convenient functions.
bwtool's functionality is subdivided into subprograms that roughly fall into three categories: data extraction, analysis, and data modification, although e.g. in the case of the matrix program or the sax program, the boundary between data extraction and analysis isn't very strong. The data modification programs all have the behavior that a bigWig is inputted and a new bigWig is outputted.
| Data Extraction | Analysis | Data modification |
|---|---|---|
| extract | aggregate | fill |
| matrix | chromgraph | lift |
| paste | distribution | remove |
| random* | find | shift |
| sax | summary | |
| window |
* available when linking to the GNU Scientific Library (GSL).
Installing bwtool should just be a matter of a few commands, hopefully. Required are libpng, libm, and zlib, all of which are included in modern linux distributions or Macs with the XCode command-line utilities installed.
To install:
$ git clone https://github.com/andypohl/bwtool.git
$ cd bwtool/
$ ./configure
$ make
$ sudo make install
If GSL is not detected in the configuration, it may be possible to install GSL in a home directory first by downloading the package from this site, unpacking the source archive, then compiling with $ ./configure --prefix=$HOME; make; make install. Once GSL is installed, it's possible then to compile with bwtool by configuring first with LDFLAGS and CFLAGS variables set:
$ ./configure --prefix=$HOME LDFLAGS=-L$HOME CFLAGS=-I$HOME
At the moment there aren't any questions.
Please direct questions to Andy Pohl.