Collection of useful Bioinformatics scripts
===========================================

Copyright (C) 2013, A. Gordon ( gordon at cshl dot edu )

Available scripts
-----------------

* bam_to_bigwig - Create BigWigs (coverage plots) from a BAM file (stranded or non-stranded)
* bam_to_genome_size - Create a 'genome-size' file based on BAM file header.
* bam_to_genomecov_tabix - Create BedGraph+BigWig+Tabix from a BAM file.
* get_region_coverage - Extract coverage for a specific region, for easy plotting.
* sam_to_bambai - Create Sorted BAM + BAI files from a SAM file.
* revcomp - Reverse-Complement a field in a text file.

PREREQUISITES
-------------

* samtools
* bedtools
* bin_scripts ( https://github.com/agordon/bin_scripts )


INSTALLATION
------------

When using the released tarball version:

 $ tar -xzvf bioinfo_bin_scripts-X.Y.Z.tar.gz
 $ cd bioinfo_bin_scripts-X.Y.Z
 $ ./configure
 $ make
 $ sudo make install

When using the GIT repository:

 $ git clone git://github.com/agordon/bioinfo_bin_scripts.git
 $ cd bioinfo_bin_scripts
 $ ./bootstrap.sh
 $ ./configure
 $ make
 $ sudo make install


SOURCE
------
See here: https://github.com/agordon/bioinfo_bin_scripts

LICENSE
-------
AGPLv3+