==================================================================== README file for PARE (v0.08)

Changes

- important bug fix during FDR computation in the previous version (v0.07).

- now user can control the stringency level at which to search for NFRs - using the -l parameter.

- now performs normalization of read coverage (sequencing depth normalization) after removing the PCR duplicates.

- since v0.06 PARE supports one or more BAM files (replicates) as input. Previous versions of PARE (0.01 - 0.05) supports only two BAM files (replicates) as input. In practical terms, -j parameter is deprecated and -p parameter requires an argument now.

Description

PARE is a computational method to Predict Active Regulatory Elements (enhancers and promoters). It implements a novel approach to detect Peak-Valley-Peak (PVP) pattern defined based on H3K4me1 and H3K4me3 signal at enhancers and promoters, respectively.

- Genomic regions enriched for H3K4me1 PVP pattern are predicted as active enhancers.

- Genomic regions enriched for H3K4me3 PVP pattern are predicted as active promoters.

Version

0.08

Citation

Please cite:

Pundhir S, Bagger FO, Lauridsen FB, Rapin N, Porse BT. (2016) Peak-valley-peak pattern of histone modifications delineates active regulatory elements and their directionality. Nucleic Acids Res. [PMID: 27095194].

Programs and datasets

Generally, the user would be interested in following two scripts:

- pare: it is the main script to detect enhancers or promoters based on input BAM files (H3K4me1 - enhancers; H3K4me3 - promoters).

- bed2direction: this script is used to detect directionality of stable transcription at promoter regions, provided as input in BED format.

An example dataset and expected results are available at:

- http://servers.binf.ku.dk/pare/download/test_run/

Installation

1. To install PARESuite, download PARESuite.tar.gz and unpack it. A directory, PARESuite will be created

    tar -zxvf PARESuite.tar.gz

2. Now compile and create executable blockbuster

    make or make all

3. Export environment variable 'PAREPATH' containing path to PARESuite installation directory

    export PAREPATH=<path to PARESuite installation directory>

4. Add 'PAREPATH' to your 'PATH' environment variable

    export PATH=$PATH:$PAREPATH/bin

5. Add 'PAREPATH' to your 'PERL5LIB' environment variable

    export PERL5LIB=$PERL5LIB:$PAREPATH/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.

1. Install the needed perl modules

    sudo cpan Tie::IxHash Statistics::Basic

2. 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"))

3. 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

4. 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

5. 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

6. 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

7. 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

PARESuite is called with the following parameters

pare -i <BAM file(s)> [OPTIONS]

Example

An usage example of PARESuite is shown below. As input, the method requires mapped reads in BAM format. An example dataset and expected results are available at http://servers.binf.ku.dk/pare/download/test_run/

pare -i data/h3k4me1_helas3_Rep1.bam,data/h3k4me1_helas3_Rep2.bam -o results -m hg19 -p 10 &> pare.log

Input

As input, the method requires one or more BAM files correspondng to each replicate of H3K4me1 (enhancer prediction) or H3K4me3 (promoter prediction) ChIP-seq experiment. The name of the input file(s) should be formatted as

Input file name (replicate 1): <unique id><Rep1>.bam (example: h3k4me1_Rep1.bam)

Input file name (replicate 2): <unique id><Rep2>.bam (example: h3k4me1_Rep2.bam)

.

.

.

Input file name (replicate N): <unique id><RepN>.bam (example: h3k4me1_RepN.bam)

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 PARESuite are presented in two text files:

a) 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

b) RESULTS.UCSC: file to view the enhancer and promoter regions in UCSC browser

More info

for more and latest information, please refer to http://spundhir.github.io/PARE/ or http://servers.binf.ku.dk/pare/

License

PARE: a computational method to Predict Active Regulatory Elements using histone marks

Copyright (C) 2015  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/>.

PARE

Install / Use

README