Running ATAC-Seq pipeline from ENCODE

Question

[siu]

Hi all, I want to run the ATAC-seq pipeline given on the ENCODE github page

(https://github.com/ENCODE-DCC/atac-seq-pipeline)

I have installed the pipeline using conda on centos 7 and made the input json file. But I am not able to understand that what to do after that.

I have seen a blog "https://bioinfocore.com/blogs/encode-atac-seq-analyzing-pipeline-hands-on-tutorial/" that has explained the steps required to run the pipeline but it is after installing slurm.

Can anyone help me to run the pipeline?

Thanks in advance

Answer 1

[ATpoint]

SLURM is simply a scheduler on HPC systems. You can (probably) just save the script and run it as bash that_script.sh. Alternatively, consider the nf-core ATAC-seq pipeline: https://nf-co.re/atacseq