faireanalysis

faireanalisys is a tool for faire-seq data analyzing of some biological samples.

The algorithm is based on learning of Hidden Markov Model and is used to comparing of samples.

Getting the latest code

To get the latest code using git, simply type:

$ git clone git://github.com/baton2809/EM.git

Installing

To install faireanalysis run:

$ python setup.py install

in the source code directory.

Preparing

Make sure you have installed the samtools, see samtools.

Move you bam files into source code directory and do sorting:

$ samtools sort XXX.bam XXX.sorted

and then make index:

$ samtools index XXX.sorted.bam

for each file.

Running

To run the tool without arguments do:

$ python -m fairy

Use --help to learn more:

$ python -m fairy --help

Format to run for example:

$ python -m fairy --gr1=ENCFF000TJP,ENCFF000TJR --gr2=ENCFF000TJJ,ENCFF000TJK --chr=chr2,chr3

Uninstall

To uninstall call:

$ chmod u+x cleanup
$ ./cleanup