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

High-throughput, genome-wide, translocation sequencing (HTGTS) pipeline. More documentation about the pipeline itself can be found here

Table of Contents

• Using HTGTS docker image
  • Singularity
    • Pull HTGTS image from DockerHUB
    • Run container
    • Inspect container
  • Docker
    • Pull HTGTS image from DockerHUB
    • Run container
    • Inspect container
  • Build HTGTS docker image
    • Build docker image
    • Push docker image to Docker HUB
    • Convert cached docker image to singularity (for local testing)

Singularity

Pull HTGTS image from data server

singularity pull docker://sandrejev/htgts:latest

Run container

Before running HTGTS pipeline you will need to obtain genome (fasta), bowtie index (.bt2), chromosome sizes (.chrom.sizes), annotation (ChromInfo.txt, cytoBand.txt, refGene.bed). For mm9, mm10 and hg19 these can be downloaded automatically with download command. The default location is to download these files to ./genomes folder in the current directory, but this can be changed using GENOME_DB environment variable. You can either set this variable in your .bashrc or .bash_profile file or prepend all commands in this tutorial like this GENOME_DB=./new_location singularity [command]

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

Run HTGTS pipeline. Keep in mind that refGene annotation file (refGene.bed) is created automatically for you from geneRef.gtf

singularity exec -B `pwd` htgts_latest.sif TranslocPreprocess.pl tutorial_metadata.txt preprocess --read1 pooled_R1.fastq.gz --read2 pooled_R2.fastq.gz --threads 16
singularity exec -B `pwd` htgts_latest.sif TranslocWrapper.pl tutorial_metadata.txt preprocess/ results/ --threads 8

Detect translocation peaks using MACS2

singularity exec -B `pwd` htgts_latest.sif tlx2BED-MACS.pl
singularity exec -B `pwd` htgts_latest.sif macs2

Inspect container

singularity shell htgts_latest.sif

Docker

Pull HTGTS image from DockerHUB

docker pull sandrejev:htgts

Run container

Before running HTGTS pipeline you will need to obtain genome(fasta), bowtie index (.bt2), chromosome sizes (.chrom.sizes) and annotation. For mm9, mm10 and hg19 these can be downloaded automatically with download command. The only exception being annotation *.bed file.

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

Run HTGTS pipeline. Keep in mind that refGene annotation file (refGene.bed) is created automatically for you from geneRef.gtf

docker run -v ${PWD}:/mount -u $(id -g ${USER}):$(id -g ${USER}) -it --entrypoint TranslocPreprocess.pl htgts tutorial_metadata.txt preprocess --read1 pooled_R1.fastq.gz --read2 pooled_R2.fastq.gz --threads 8
docker run -v ${PWD}:/mount -u $(id -g ${USER}):$(id -g ${USER}) -it --entrypoint TranslocWrapper.pl htgts tutorial_metadata.txt preprocess/ results/ --threads 8

Detect translocation peaks using MACS2

docker run -v ${PWD}:/mount -u $(id -g ${USER}):$(id -g ${USER}) -it --entrypoint tlx2BED-MACS.pl htgts
docker run -v ${PWD}:/mount -u $(id -g ${USER}):$(id -g ${USER}) -it --entrypoint macs2 htgts

Inspect container

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

Building HTGTS docker image

Build docker image

To build Docker image you need to execute

docker build --build-arg http_proxy=$http_proxy --build-arg https_proxy=$https_proxy --rm -t sandrejev/htgts:latest .

Push docker image to Docker HUB

docker login
docker push sandrejev/htgts:latest

Convert cached docker image to singularity (for local testing)

singularity cache clean
singularity pull docker-daemon:sandrejev/htgts:latest