Scripts required for the processing of FASTQ files (eg generating adjacency lists for Hi-C data)

• Python 2.7.12 (required for MACS2 in ChIP-Seq pipeline)
• Python 3.5.2 (required for iNPS in MNase-Seq pipeline)
• Python Modules:
  • mg-tool-api
  • numpy
  • h5py
  • scipy
  • matplotlib
  • TADbit
  • pysam
  • MACS2 - can be installed with pip, but runs on command line
  • rpy2
• GEMtools
• HDF5
• Bowtie2
• BWA
• SAMtools
• BS-Seeker2
• libmaus2
• BioBamBam2
• imp (for 3D modelling with TADbit)
• mcl
• R (2.9.1)
• iNPS

For a guide to the full installation procedure the see ReadTheDocs.

Directly from GitHub:

.. code-block:: none :linenos:

cd ${HOME}/code

git clone https://github.com/Multiscale-Genomics/mg-process-fastq.git

cd mg-process-fastq

Create the Python environment

.. code-block:: none :linenos:

pyenv-virtualenv 2.7.10 mg-process-fastq pip install --editable .