DNase2Hotspots Files

{\rtf1\ansi\ansicpg1252\cocoartf1138\cocoasubrtf510
{\fonttbl\f0\froman\fcharset0 Times-Roman;}
{\colortbl;\red255\green255\blue255;\red0\green0\blue255;\red255\green0\blue0;}
{\*\listtable{\list\listtemplateid1\listhybrid{\listlevel\levelnfc0\levelnfcn0\leveljc0\leveljcn0\levelfollow0\levelstartat1\levelspace360\levelindent0{\*\levelmarker \{decimal\}.}{\leveltext\leveltemplateid1\'02\'00.;}{\levelnumbers\'01;}\fi-360\li720\lin720 }{\listname ;}\listid1}}
{\*\listoverridetable{\listoverride\listid1\listoverridecount0\ls1}}
{\info
{\author sojbaek}}\margl1440\margr1440\vieww13140\viewh16740\viewkind1
\deftab720
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1

\f0\fs30 \cf0 DNase2Hotspots README\
\
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1

\fs24 \cf0 Last updated: November 2, 2012\
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1

\b \cf0 \uc0\u8232 Current Maintainer
\b0 : Songjoon Baek 	{\field{\*\fldinst{HYPERLINK "%22mailto:"}}{\fldrslt \cf2 \ul \ulc2 baeks@mail.nih.gov}}\cf3 \

\b \cf0 License
\b0 : GNU General Public License, v 3.0\
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\li720\ri0\sl288\slmult1
\cf0  \
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1

\b \cf0 Introduction\
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\fi360\ri0\sl288\slmult1

\b0 \cf0 \
 DNase2Hotspots is a software package for identifying tag-enriched genomic regions (hotspots) from DNase-seq data.  The program reads a BAM (Binary Alignment Map) file or a tab-delimited text file as input and produces a list of hotspots and associated z-scores as output.  Mappability profiles for the reference genome and repeat-masked regions are also required as input.   
\fs20 \

\fs24 \
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1

\b \cf0 Reference\
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1

\b0 \cf0 Baek S, Sung MH, Hager GL.: Quantitative analysis of genome-wide chromatin remodeling.\
Methods Mol. Biol. 833: 433-41, 2012.\
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1

\b \cf0 \
Platforms\
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1

\b0 \cf0 The software has been tested on Linux Ubuntu 11.10, Mac OS X 10.7, and Microsoft Windows 7.\
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1

\b \cf0 \
Prerequisites\
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\fi360\ri0\sl288\slmult1

\b0 \cf0 \
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\li720\fi-360\ri0\sl288\slmult1
\ls1\ilvl0\cf0 1.	At least 4 GB of RAM \
2.	BamTools (
\fs20 https://github.com/pezmaster31/bamtools
\fs24 )\
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1
\cf0 \
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1

\b \cf0 Installation\
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1

\b0 \cf0 \
\pard\tx360\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\li630\fi-270\ri0\sl288\slmult1
\cf0 1. Make a folder and unzip DNase2Hotspots.zip file into the folder. \
2. Specify \'91include\'92 and \'91lib\'92 directories after BAMTOOL_INCLUDEDIR and BAMTOOL_LIBDIR in \'91Makefile\'92.\
3. Type \'91make\'92 in the command shell to compile \'91dnase2hotspots\'92.\
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1
\cf0 \
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1

\b \cf0 Usage\
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1

\b0 \cf0 \
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\fi360\ri0\sl288\slmult1
\cf0 Example:\
   $ dnase2hotspots  example_1.cfg \
\
\'91example_1.cfg\'92 is a text file containing locations of data files, mappability files, and options.  Two example configuration files are included in the package.\
 \
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\ri0\sl288\slmult1

\b \cf0 Mappability \
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\fi360\ri0\sl288\slmult1
\cf0 \
\pard\tx720\tx1440\tx2160\tx2880\tx3600\tx4320\pardeftab720\fi360\ri0\sl288\slmult1

\b0 \cf0  A k-mer mappability file of a chromosome is a binary file that has, at each n\super th\nosupersub  byte position of the file, the occurrence frequency (values between 0 and 255) of the 5\'92-directional k-mer (starting at the position of the chromosome) in the reference genome.   Mappability files can be generated by a mappability mapping program developed by the Gerstein lab at Yale University (gerstein.org) as part of the PeakSeq package (http://archive.gersteinlab.org/proj/PeakSeq/Mappability_Map/Code/).   The filenames of the mappability profiles must be in the form of \'93Chromosome name\'94+\'94b.out\'94 such as  \'93chr1b.out\'94, \'93chr2b.out\'94, etc.
\fs20 \
}