Ataqv

Introduction

Ataqv is a toolkit for measuring and comparing ATAC-seq results, made in the Parker lab at the University of Michigan.

For more information, please check its website: https://biocontainers.pro/tools/ataqv and its home page on Github.

Versions

  • 1.3.0

Commands

  • ataqv

Module

You can load the modules by:

module load biocontainers
module load ataqv

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Ataqv on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=ataqv
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers ataqv

ataqv --peak-file sample_1_peaks.broadPeak \
    --name sample_1 --metrics-file sample_1.ataqv.json.gz \
    --excluded-region-file hg19.blacklist.bed.gz \
    --tss-file hg19.tss.refseq.bed.gz \
    --ignore-read-groups human sample_1.md.bam \
     > sample_1.ataqv.out

ataqv --peak-file sample_2_peaks.broadPeak \
    --name sample_2 --metrics-file sample_2.ataqv.json.gz \
    --excluded-region-file hg19.blacklist.bed.gz \
    --tss-file hg19.tss.refseq.bed.gz \
    --ignore-read-groups human sample_2.md.bam \
    > sample_2.ataqv.out

ataqv --peak-file sample_3_peaks.broadPeak \
    --name sample_3 --metrics-file sample_3.ataqv.json.gz \
    --excluded-region-file hg19.blacklist.bed.gz \
    --tss-file hg19.tss.refseq.bed.gz \
    --ignore-read-groups human sample_3.md.bam \
     > sample_3.ataqv.out

mkarv my_fantastic_experiment sample_1.ataqv.json.gz sample_2.ataqv.json.gz sample_3.ataqv.json.gz