README.md

In aiminy/AtacSeq:

Instruction for setting and using AtacSeq pipeline

Install some required tools

# install the following software

# Anaconda3
# Download Anaconda 4.4.0 For Linux for Python 3.6 version from https://www.anaconda.com/download/
# After downkloading, run the following:
bash Anaconda3-4.4.0-Linux-x86_64.sh

# To use Python3.6 you installed locally, you need to unload default python/2.7.3 firstly
module unload python/2.7.3

# Other required software
conda install -c bioconda cutadapt
conda install -c bioconda sambamba
conda install -c conda-forge -c bioconda samtools bzip2
conda install -c bioconda picard
conda install -c bioconda idr
#pip install --upgrade --force-reinstall numpy
conda install -c conda-forge numpy

# To install pysam in your current conda environment, type:

# add channels
conda config --add channels r
conda config --add channels bioconda
conda config --add channels conda-forge

# list available channels
# less ~/.condarc

conda install pysam

Test environment

module rm python/2.7.3
conda install -c conda-forge -c bioconda samtools bzip2
conda install htslib

• To install

R -e 'library(devtools);install_github("aiminy/AtacSeq")'

• To install genome data for a specific genome(hg19)

R -e 'library(DoGs);library(AtacSeq);AtacSeq:::submitJob("hg19","/scratch/projects/bbc/aiminy_project/AtacSeq")'

To check if atac is installed

#change to /nethome/axy148/atac_dnase_pipelines directory, and check
bds atac.bds

• To test

# On cluster
R -e 'library(DoGs);library(AtacSeq);AtacSeq:::submitJob4testAtacSeq0()'

#On local linux machine
R -e 'library(DoGs);library(AtacSeq);AtacSeq:::testAtacSeqNonCluster("/media/aiminyan/DATA/AtacSeq_Input","/media/aiminyan/DATA/AtacSeq_Output")'

# On Macs
R -e 'sample.info = "~/pegasus/Project/Alejandro_AtacSeq/ATACSeq_sample_mapping.csv";title = "IL-2vsPBS";species = "mm10";input.fq.dir ="~/pegasus/Project/Alejandro_atac/DATA/Formatted";output = "~/pegasus/Project/Alejandro_AtacSeq";library(DoGs);library(AtacSeq);AtacSeq:::testAtacSeqNonCluster2(sample.info,input.fq.dir,title,species,output)'

On linux to run

# install mm10 genome data
R -e 'library(DoGs);library(AtacSeq);AtacSeq:::installAtacSeq("mm10","/media/pegasus/Project/Alejandro_AtacSeq")'

# run for  IL2-at-16
R -e 'sample.info = "/media/pegasus/Project/Alejandro_AtacSeq/ATACSeq_sample_mapping.csv";title = "IL-2vsPBS";species = "mm10";input.fq.dir ="/media/pegasus/Project/Alejandro_atac/DATA/Formatted";output = "/media/pegasus/Project/Alejandro_AtacSeq";library(DoGs);library(AtacSeq);AtacSeq:::testAtacSeqNonCluster2(sample.info,input.fq.dir,title,species,output)'

# On linux to run other samples
R -e 'sample.info = "/media//pegasus/Project/Alejandro_AtacSeq/ATACSeq_sample_mapping.csv";species = "mm10";input.fq.dir ="/media/pegasus/Project/Alejandro_atac/DATA/Formatted";output = "/media/pegasus/Project/Alejandro_AtacSeq";AtacSeq:::testAtacSeqNonCluster3(sample.info,input.fq.dir,species,output)'

Upload results from pegausus to dropbox

git clone https://github.com/andreafabrizi/Dropbox-Uploader.git
chmod +x Dropbox-Uploader/dropbox_uploader.sh
Dropbox-Uploader/dropbox_uploader.sh upload /media/pegasus/Project/Alejandro_AtacSeq Alejandro_AtacSeq_uploaded_2

aiminy/AtacSeq documentation built on May 22, 2019, 4:39 p.m.