Cistrome ChiLin

It is a python package for one-in-all solution of processing ChIP-seq and DNase-seq data.

Quick Start

See if you have gcc, g++, java, R, python-dev installed (http://cistrome.org/chilin/Installation.html#dependent-software-list).

First, clone:

git clone https://github.com/cfce/chilin

then install through with the system-wide python and pip, e.g., /usr/bin/python or /usr/local/bin/python,

wget -c https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

conda create -n chilin_env python=2
conda activate chilin_env
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

conda install bwa=0.7.13 samtools=0.1.19 bedtools=2.17.0 seqtk ucsc-bedclip ucsc-bedgraphtobigwig ucsc-wigcorrelate ucsc-wigtobigwig fastqc numpy macs2=2.1.0 bioconductor-seqlogo 

easy_install pip
python setup.py install

source virtual environment and use:

chilin -h

And download the reference files, and test on demo/foxa1.

# change to default directory
mkdir -p db
cd db

# download genome specific annotation to chilin/db and uncompress
# http://cistrome.org/chilin/Appendix.html#get-dependent-data
cd chilin/db && wget -c http://cistrome.org/chilin/_downloads/hg38.tgz

# all hg19 reference data
wget -c http://cistrome.org/chilin/_downloads/hg19.tgz
wget -c http://cistrome.org/chilin/_downloads/hg19.tgz.md5 ## check md5
md5sum -c hg19.tgz
tar xvfz hg19.tgz
# download mycoplasma for judgement of contamination in your samples
wget -c http://cistrome.org/chilin/_downloads/mycoplasma.tgz
wget -c http://cistrome.org/chilin/_downloads/mycoplasma.tgz.md5
md5sum -c mycoplasma.tgz.md5
tar xvfz mycoplasma.tgz

cd .. && python setup.py install
cd demo && bash foxa1

Usage

Demo data command is as follows:

   chilin  simple -p narrow -t foxa1_t1.fastq  -c foxa1_c1.fastq -i local -o local -s hg19  --skip 10,12 --dont_remove

See skip_ option for details.

This is major and the easiest mode to run ChiLin for single end data with default bwa mapper, for single end data using comma to separate sample replicates for IP and input ChIP-seq sample:

  chilin  simple -u your_name -s your_species --threads 8 -i id -o output -t treat1.fastq,treat2.fastq -c control1.fastq,control2.fastq  -p narrow -r tf

For pair end data, use semicolon to separate sample replicates, use comma to separate pairs, do not forget to add quotes(") of your sample file path:

chilin simple --threads 8 -i H3K27me3_PairEnd -o H3K27me3_PairEnd -u you -s mm9 -t "GSM905438.fastq_R1.gz,GSM905438.fastq_R2.gz" -c "GSM905434.fastq_R1.gz,GSM905434.fastq_R2.gz;GSM905436.fastq_R1.gz,GSM905436.fastq_R2.gz" -p both --pe

Currently, only bwa support pair end processing. bwa supports both fastq.gz and fastq file, bowtie only support fastq file, the pipeline should use the corresponding aligner's genome index configured in the configuration files. For library contamination evaluation, user need to fill in the bwa genome index for the e.coli or mycoplasma or other species' genomes.

Update the configuration

If you modify the code or update any part of the configuration file chilin.conf.filled, such as different aligner's genome index, union DHS BED file, reinstall the package itself only.

python setup.py install 

TODO

An conda or docker version is under development.

PdfLatex Troubleshooting

If any error of the dependent software occur, try to upgrade the corresponding software. Those warnings generated in pdflatex step is ok. There is one known issue of mm9 chrom-info in CentOS. ChiLin is suggested to be used under Ubuntu. If sys_platform error occurs, uninstall the system setuptools and install the latest setuptools manually. Later pdflatex is not incompatible with the macro used in the latex report, update with sudo apt install cm-super && updmap.

Documentation

full documentation: http://cistrome.org/chilin

github wiki: https://github.com/cfce/chilin/wiki