PuFFIN

A Parameter-free Method to Build Genome-wide Nucleosome Maps from Paired-end Sequencing Data

Dowload: type "git clone https://github.com/ucrbioinfo/PuFFIN"

Requires Python 2.7, numpy, pylab, and pickle

A sample input file is provided in example.bam

The input file for the tool should contain the reads only for one chromosome (or a contig) and is in a BED format obtained by simply parsing the BAM/SAM file (see bam2bedpe.sh for example).

Usage

Given that input reads are in input.bam, that contain only reads for particular chromosome

./bam2bedpe.sh input.bam > input.bed

python Run.py input.bed

The output will be printed in input.bed.nucs using next column format: <"Fuzziness">

For more details visit http://alumni.cs.ucr.edu/~polishka/indexPuffin.html

Questions: email Anton Polishko polishka@cs.ucr.edu