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

mg-process-fastq

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

Requirements

  • Python 2.7.12 or 3.6+
  • 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

Installation

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 .