Running ATAC-Seq pipeline from ENCODE
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2.4 years ago
siu ▴ 160

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

ATAC Genomics python GENOME R • 1.3k views
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2.4 years ago
ATpoint 80k

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

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