README file for findNFR (v0.01)
Description
findNFR is a computational method to predict Nucleosome Free Regions corresponding to input genomic regions in BED format.
Version
0.01
Citation
Programs and datasets
Installation
To install findNFR, download findNFR.tar.gz and unpack it. A directory, findNFRSuite will be created
tar -zxvf findNFR.tar.gz
Now compile and create executable blockbuster
make or make all
Export environment variable 'FINDNFRPATH' containing path to findNFR installation directory
export FINDFRPATH=<path to findNFR installation directory>
Add 'FINDNFRPATH' to your 'PATH' environment variable
export PATH=$PATH:$FINDNFRPATH/bin
Add 'FINDNFRPATH' to your 'PERL5LIB' environment variable
export PERL5LIB=$PERL5LIB:$FINDNFRPATH/share/perl/
To permanently add or update the environment variable(s), add the last three export commands in your ~/.bashrc file
Dependency
We assume that the following programming platforms are installed and working: perl, R, and gcc. Besides, following packages should be installed.
Install the needed perl modules
sudo cpan Tie::IxHash Statistics::Basic
R modules are installed by entering R (type R on the cmdline) and then enter the following three commands (follow the instructions on the screen):
install.packages(c("ggplot2", "gridExtra", "optparse", "randomForest", "e1071"))
source("http://bioconductor.org/biocLite.R")
biocLite(c("DESeq"))
download samtools from http://sourceforge.net/projects/samtools/files/samtools/1.2/samtools-1.2.tar.bz2/download, go to the download location and do
tar xjf samtools-1.2.tar.bz2
cd samtools-1.2
make -j10 prefix=$HOME install
download bedtools from https://github.com/arq5x/bedtools2/releases/download/v2.23.0/bedtools-2.23.0.tar.gz, go to the download location and do
tar xzf BEDTools.v2.23
cd bedtools-2.23.0/
make -j 10
cp bin/* $HOME/bin
download featureCounts (subread) from http://sourceforge.net/projects/subread/files/subread-1.4.6-p4/, go to the download location and do
tar xzf subread-1.4.6-p4-Linux-x86_64.tar.gz
cd subread-1.4.6-p3-Linux-x86_64
cp bin/featureCounts $HOME/bin
download bedGraphToBigWig from http://hgdownload.soe.ucsc.edu/admin/exe/ for your operating system, go to the download location and do
cp bedGraphToBigWig $HOME/bin
chmod 755 $HOME/bin/bedGraphToBigWig
download macs2 version 2.1.0 from https://github.com/taoliu/MACS/, go to the download location and install as mentioned in INSTALL.rst file
Usage
findNFR is called with the following parameters
findNFR -i <BAM file(s)> -k <BED file> [OPTIONS]
Example
findNFR -i data/histone_Rep1.bam,data/histone_Rep2.bam -k input.bed -o results -m hg19 -p 10 &>findNFR.log
Input
- BAM file(s) corresponding to each replicate(s)
- BED file containing genomic coordinates of regions of interest
The chromosome identifier in the input BAM files should start with chr, for example as chrY and not like Y.
Output
The results from the findNFR are presented in two text files:
- RESULTS.TXT: main result file in BED format
For easy access, the html version of this file (RESULTS.HTML) is also available within the output directory
- RESULTS.UCSC: file to view the enhancer and promoter regions in UCSC browser
More info
License
findNFR: a computational method to Predict Nucleosome Free Regions using histone marks
Copyright (C) 2017 Sachin Pundhir (pundhir@binf.ku.dk)
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.