ChIPseqTools

1. Overview

This repository contains several utility tools for ChIP-seq and other epigenome analysis. These programs are written in ANCI C and C++11 using Boost library.

2. Install

2.1. Docker image

We recommend to use the latest Docker image from DockerHub.

2.1.1. Docker

To use docker command, type:

docker pull rnakato/ssp_drompa
docker run -it --rm rnakato/ssp_drompa <command>

Note: When using the docker image, it is necessary to mount the directory by -v option to access the input files as follows:

docker run -it --rm -v $(pwd):/mnt rnakato/ssp_drompa parse2wig+ \
         -i /mnt/ChIP.bam -o ChIP --odir /mnt/parse2wigdir+ --gt /mnt/genometable.txt

This command mounts the current directory to /mnt directory in the container. Please see also the document of Docker.

2.1.2. Singularity

Singularity can also be used to execute the docker image:

singularity build ssp_drompa.sif docker://rnakato/ssp_drompa
singularity exec ssp_drompa.sif <command>

Singularity mounts the current directory automatically. If you access the files in the other directory, please mount by --bind option, for instance:

singularity exec --bind /work ssp_drompa.sif <command>

This command mounts /work directory.

2.2. Building from source

2.2.1. Install required libraries

for Ubuntu:

sudo apt install git build-essential libboost-all-dev libcurl4-gnutls-dev ibgtkmm-3.0-dev \
                 libgsl-dev liblzma-dev libz-dev libbz2-dev libgzstream0 libgzstream-dev cmake

for CentOS:

sudo yum -y install git gcc-c++ boost-devel

On Mac:

 brew install gsl gtk gtkmm pkgconfig curl xz zlib boost cmake gzstream

2.2.2. Install

git clone --recursive https://github.com/rnakato/ChIPseqTools.git
cd ChIPseqTools
make

2.2.3. Add the PATH environment variable

export PATH = $PATH:(PATH_TO_ChIPseqTools)/ChIPseqTools/bin

2.2.4 (Optional) Update repository

git pull origin master
git submodule foreach git pull origin master

3. Usage

3.1. gtf2refFlat

3.2. compare_bs

output shared peaks between bed1 and bed2

compare_bs -1 <bed1> -2 <bed2> -and

output bed1-unique peaks

compare_bs -1 <bed1> -2 <bed2> -not

output stats only

compare_bs -1 <bed1> -2 <bed2> -and -nobs

include neighboring peaks within 5kbp as overlaped peaks

   compare_bs -1 -2 -and -l 5000

consider peak summit (default: whole peak region)

   compare_bs -1 -2 -and -maxposi

3.2. compare_bed2tss

gene (gtf) and peaks

compare_bed2tss -g <gtf> -b <peak> --gt <genome table>

gene (refFlat) and peaks

compare_bed2tss -g <refFlat> --refFlat -b <peak> --gt <genome table>

comare with gene body

compare_bed2tss -g <gtf> -b <peak> --gt <genome table> --mode 1

proportion of peaks against whole genome

compare_bed2tss -g <gtf> -b <peak> --gt <genome table> --mode 2

proportion of peaks against whole genome (distinguish exon and instron)

compare_bed2tss -g <gtf> -b <peak> --gt <genome table> --mode 2 --intron

3.3. compare_bed2loop

Usage: compare_bed2loop [option] --bed1 <1st bed> --bed2 <2nd bed> --loop <loop file> -o <output> -gt <genome_table>
Options:
   --bed1 arg               1st bed file
   --bed2 arg               2nd bed file
   --loop arg               Loop file
   -l [ --length ] arg (=0) Extend length for overlap
   --gt arg                 Genome table (tab-delimited file describing the name
                            and length of each chromosome)
   --nobs                   do not output the overlapped loop list
   --hiccups                HICCups format as input (default: Mango)
   -h [ --help ]            print this message

3.4. peak_occurance

3.5. multibed2gene

3.6. mergebed2CRM

  mergebed2CRM -i <bs file> -name <name> [-i <bs file> -name <name> ...]
     -l: extend length (default:0)
     -n: number of peaks for clustering (default:3000, setting 0 means use all peaks)
     -qnt: quantitative analysis

3.6. FRiR

Repeat analysis.

   FRiR [option] -r <repeatfile> -i <inputfile> -o <output> --gt <genome_table>

is the RepeatMasker file downloaded from the UCSC genome browser. FRiR can allow a gzipped repeat file.