Repli-Seq pipeline package (Wei, Pei-Chi group; DKFZ)

Global Run-On Sequencing (GRO-Seq) pipeline for analyzing transcription activity of genes from engaged RNA polymerase.

Table of Contents

• Using Repli-seq docker image
  • Singularity
    • Pull Repli-seq image from DockerHUB
    • Run container
    • Inspect container
  • Docker
    • Pull Repli-seq image from DockerHUB
    • Run container
    • Inspect container
  • Build Repliseq-seq docker image
    • Download required packages and files
    • Build docker image
    • Push docker image to Docker HUB
    • Convert cached docker image to singularity (for local testing)

Singularity

Pull Repli-seq image from data server

singularity pull docker://peggyweidkfz/repliseq:latest

Run container

Before running Repli-seq pipeline you will need to obtain genome(fasta). For mm9, mm10 and hg19 these can be downloaded automatically with download command.

singularity exec -B `pwd` repliseq.sif download mm10

Run Repli-seq pipeline

 
singularity exec -B `pwd` repliseq.sif align -m ~/Workspace/Datasets/Repliseq/raw/B400_RS_001_23911/23911_meta.tsv -g ~/Workspace/genomes/mm10/mm10 -o ~/Workspace/Datasets/Repliseq -t 32 --fastq-dir ~/Workspace/Datasets/Repliseq/raw/B400_RS_001_23911
singularity exec -B `pwd` repliseq.sif coverage -m ~/Workspace/Datasets/Repliseq/raw/B400_RS_001_23911/23911_meta.tsv -o ~/Workspace/Datasets/Repliseq --binsizes 30000,40000,60000

Inspect container

singularity shell repliseq.sif

Docker

Pull Repli-seq image from DockerHUB

docker pull peggyweidkfz:repliseq

Run container

Before running Repli-seq pipeline you will need to obtain genome(fasta). For mm9, mm10 and hg19 these can be downloaded automatically with download command.

docker run -v ${PWD}:/mount -u $(id -g ${USER}):$(id -g ${USER}) -it --entrypoint download repliseq mm10

Run groseq pipeline. Keep in mind that annotation file (-a flag) is created automatically for you from geneRef.gtf

docker run -v ${PWD}:/mount -u $(id -g ${USER}):$(id -g ${USER}) -it --entrypoint align repliseq -m ~/Workspace/Datasets/Repliseq/raw/B400_RS_001_23911/23911_meta.tsv -g ~/Workspace/genomes/mm10/mm10 -o ~/Workspace/Datasets/Repliseq -t 32 --fastq-dir ~/Workspace/Datasets/Repliseq/raw/B400_RS_001_23911
docker run -v ${PWD}:/mount -u $(id -g ${USER}):$(id -g ${USER}) -it --entrypoint coverage repliseq -m ~/Workspace/Datasets/Repliseq/raw/B400_RS_001_23911/23911_meta.tsv -o ~/Workspace/Datasets/Repliseq --binsizes 30000,40000,60000

Inspect container

docker run -v ${PWD}:/mount -u $(id -g ${USER}):$(id -g ${USER}) -it --entrypoint bash repliseq

Building Repli-seq docker image

Build docker image

To build Docker image you need to execute

docker build --squash --build-arg http_proxy="http://www-int2.inet.dkfz-heidelberg.de:80" --build-arg https_proxy="http://www-int2.inet.dkfz-heidelberg.de:80" --progress=plain --rm -t peggyweidkfz/repliseq:latest .

Push docker image to Docker HUB

docker login
docker push peggyweidkfz/repliseq:latest

Convert cached docker image to singularity (for local testing)

singularity pull docker-daemon:peggyweidkfz/repliseq:latest