Code for mapping DNA (with BWA) and RNA (with Tophat) to personal genomes from the chromatin variation project (Kasowski et al., 2013). 
Forked from sofiakp/ase.

Main update: Code now works on the scg3 cluster (i.e. on an sge-based cluster).

INSTALLATION
============

1. Get the code. Assume you want the code to be placed in a directory called mappingDir.
cd mappingDir
git clone https://github.com/oursu/Personal_genome_mapping

2. Define the CODEDIR variable to be the directory where you have cloned the code (use full paths).
CODEDIR=mappingDir/Personal_genome_mapping/

3. Setup ase code

- Load modules boost and cmake
For instance, for scg3, do the following 2 commands:
module add boost/1.51.0
module add cmake/2.8.11.2

- then configure and make
cd ${CODEDIR}/new_ase_code/ase_cpp
chmod 711 configure.sh
./configure.sh
make

4. Modify the bashrc file, to point the code to samtools and other relevant packages used here.
The file to modify is:
${CODEDIR}/Personal_genome_mapping/personal_genome_mapping.bashrc 

Congratulations. You are now ready to map to personal genomes!

RUNNING CODE
============

An example for how to run the code, and what files are required is found in testFiles/testRun.sh
The code can be run by calling the main function, MAPPING_wrapper.py. To see a list of required arguments, type:
python ${CODEDIR}/MAPPING_wrapper.py -h

Information from original package:
=================================
new_ase_code/bin
Mostly preprocessing stuff (alignment/cleaning up of reads, peak calling, signal track
generation, QC etc). In many cases there's two scripts with similar names (eg. alignSample.sh and
alignBatch.sh). In these cases, the "Sample" script does the actual work. The "Batch" script reads
metadata (such as cell line name, factor name etc) and submits jobs that call the "Sample" script.

new_ase_code/ase/python
Code for creating personal genomes (the add*Snps* files). Various other utilities.