Created: 2012-03-26 14:20
Updated: 2015-06-24 14:38

README.md

Tools for 4C data analysis

As of now this project is not set up to work with setuptools/distribute. Instead, it is a self-contained directory that can be directly executed with python, i.e.

python 4c

Global help text can be displayed with

python 4c -h

The tools are setup as subcommands

python 4c {make-index,align,fragcount,bin}

and help for each can be obtained with

python 4c subcommand -h

Subcommand descriptions (in brief):

Subcommands listed in order relevant for analyzing paired end solexa 4C experiments:

make-index Create bowtie index of restriction fragments (with flanking region)
align Align 4c pairs to restriction fragment index
fragcount Summarize the number of reads per detected fragment
bin test help text

Dependencies

###Python libraries:

  • argparse (either python >= 2.7 or backported separate library)
  • Biopython
  • pybedtools
  • pysam
  • numpy

###External executables on path:

  • bowtie and bowtie-build
  • samtools
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