Splicing analysis toolkit for RNA-SEQ
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bin
spanki
README
analysis_commands.sh
gpl-3.0.txt
license.txt
plotting_code.R
setup.py
simulation_example.txt

README

Splicing Analysis Kit (Spanki) 
--       --       --

Most recent release: 0.5.0

Overview
==============
Spanki is a set of tools to facilitate analysis of alternative splicing from
RNA-SEQ data.  Drawing from multiple published and novel analysis methods,
Spanki compiles quantitative and qualitative information about junction
alignments and splicing events.  The basic functions of Spanki are to assess
confidence in junction alignments, and to quantify and compare splicing events.


Getting started
===============

Please see the manual page for details about installing and usage:
 http://www.cbcb.umd.edu/software/spanki/manual.html

Spanki has been tested on Mac OSX >= 10.6 and Ubuntu Linux 10.04

Prerequisites
---------------

Python modules
~~~~~~~~~~
Spanki requires the following Python packages (Python will attempt to install them for you):

pyfasta
pysam
numpy
Biopython
scikits.statsmodels
fisher

If you encounter problems getting numpy and scipy installed together, we recommend installing the ENTHOUGHT python distribution (http://enthought.com/products/epd.php). 

Other required programs
~~~~~~~~~~
samtools http://samtools.sourceforge.net/
Cufflinks (Spanky uses the gtf_to_sam utility to create a sam representation of a gtf reference) http://cufflinks.cbcb.umd.edu

Required for splicing analysis:
AStalavista (or a precomputed splicing event file) http://sammeth.net/confluence/display/ASTA/Home

Installation
---------------
Clone this repo:
git clone git://github.com/dsturg/Spanki

Then use the python install process:
	sudo python setup.py install

OR:
Download the most stable release (See https://github.com/dsturg/Spanki/downloads)
Decompress and install as described above


Example data
---------------
A test data set is available to try out the basic Spanki commands.
You can download it here (~250 MB download):
http://www.cbcb.umd.edu/software/spanki/testdata.tar.gz

See the file simulation_example.txt for commands to walk
through the simulation steps, using the test data.

See the file analysis_commands.sh for an example
run-through for splicing analysis


Questions
---------------
Contact Dave Sturgill
dave.sturgill@gmail.com