mirror_seq 0.2.2

What is it
==========

Mirror-seq is a assay invented by `Zymo
Research <http://zymoresearch.com>`__ to detect
`hydroxymethylation <>`__ (hmc) in genomes using `bisulfite
sequencing <>`__. This analysis tool helps biologists to analyze
sequencing data. It takes Fastq files from sequencers and generate
hydroxymethylation ratio for each CpGs.

What's included
===============

We provide two way to do analysis. If you are new or like to do a quick
analysis, the **Qucik Start** below is the total solution you would
like. It set up the environment for you and has a simple workflow -
trimming, alignment, hydroxymethylation calling. Just type in one
command. You will find results in your workplace in several hours.

If you are bioinformatics expert or anyone eager to try different
parameters, we also provide the component of initial fill-in nucleotides
trimming () and the final hydroxymethylation calling () parts as
standalone program. You can plug in your favor QC and adapter trimming
software and alignment software with your homemade parameters. Please
fellow the **installation** section below for more details.

Quick Start
===========

We created a `Docker <>`__ image to solve the dependency problem and
scientists can use either Windows, MacOS, or Linux to run the analysis.

Install Docker
--------------

Find your OS and follow the installation instructions of
`Windows <https://docs.docker.com/windows/step_one/>`__,
`MacOS <https://docs.docker.com/mac/step_one/>`__, and
`Linux <https://docs.docker.com/linux/step_one/>`__ from Docker's
official website.

Run Mirror-seq
--------------

You need to create a workplace directory (``<YOUR WORKPLACE>``) and put
the following files inside: \* Read 1 and Read 2 Fastq files. \* Genome
index (We provide `human index <>`__. Unzip the file after downloading.)

::

docker run -it --rm -v <YOUR WORKPLACE>:/workplace \
zymoresearch/mirror-seq \
-1 <READ 1 FILENAME> -2 <READ 2 FILENAME> \
-g <GENOME INDEX FOLDER NAME> --bed

Notes:
------

Although it is super easy to run the analysis tool, there are several
things you need to know in order to run it smoothly. \* The alignment
part is memory intensive and CPU intensive.
`Bismark <http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/>`__,
the aligner we used in our tool, suggests at least 5 cores and > 16GB of
RAM. \* Usually Fastq files are several GB even with compression. In the
first trimming part, the tool could need up to 3 times large as the
original input. Please make sure your workplace has enough storage
space.

installation
============

Dependencies
============

Python (2.7)
------------

- `NumPy <http://www.numpy.org/>`__: 1.7.0
- `pandas <http://pandas.pydata.org/>`__: 0.18.0
- `numexpr <https://github.com/pydata/numexpr>`__: 2.5.2
- `pysam <http://pysam.readthedocs.org/en/latest/api.html>`__: 0.9.0
- `cutadapt <http://cutadapt.readthedocs.org/en/stable/guide.html>`__:
1.9.1
- `PyTables <http://www.pytables.org/>`__: 3.2.2

Bioinformatics software
-----------------------

- `bedToBigBed <http://hgdownload.cse.ucsc.edu/admin/exe/>`__
- `bedSort <http://hgdownload.cse.ucsc.edu/admin/exe/>`__
- `Trim
Galore! <http://www.bioinformatics.bbsrc.ac.uk/projects/trim_galore/>`__:
0.3.7
- `bowtie2 <http://bowtie-bio.sourceforge.net/bowtie2/index.shtml>`__:
2.2.6
- `Bismark <http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/>`__:
0.14.5