jianhong / atacseqpipe

ATAC-seq analysis Pipeline

ATACseqPipe

ATAC-seq analysis Pipeline

Install

Docker

Please set your docker disk image size > 120G in Preference>Disk>Disk image size. Or set the blastdb to a attached disk for image.

cd ~
docker pull jianhong/atacseqpipe:latest
mkdir tmp4atacseqpipe
docker run -it --rm -v ${PWD}/tmp4atacseqpipe:/volume/data \
       jianhong/atacseqpipe:latest bash

## In the docker
cd /volume/data
git clone https://github.com/jianhong/ATACseqPipe.git
cd ATACseqPipe
bash PrepareBlastDB.sh
bash PrepareGenome.sh -s danRer10

Run

Docker

Please copy your data into tmp4atacseqpipe folder in following format:

fastq-|
      |--condition1-|
      |             |--rep1.fastq.gz
      |             |--rep2.fastq.gz
      |             |-- ...
      |             |--repN.fastq.gz
      |--condition2-|
      |             |--rep1.fastq.gz
      |             |--rep2.fastq.gz
      |             |-- ...
      |             |--repN.fastq.gz
      |...

And in the docker:

source /opt/conda/bin/activate jo_ATACseqPipe
bash ATACseq.sh