ataqv
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'ataqv' Versions
- 1.3.0
Link to section 'Commands' of 'ataqv' Commands
- ataqv
Link to section 'Module' of 'ataqv' Module
You can load the modules by:
module load biocontainers
module load ataqv
Link to section 'Example job' of 'ataqv' Example job
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