how to run and use the ENCODE ATAC-seq pipline

Question

[cwwong13]

I know the questions seem naive (I am working on slurm environment):

1. What command should I use to run the ENCODE ATAC seq pipeline?
2. Which output file should be used for downstream analysis (and where to locate them)?

My goal is to further analysis the data with ChIPseeker, Diffbind etc.

Indeed, I have found the code in this tutorial and this tutorial by NIH helpful (at least, I can run the pipeline now). However, the pipeline generates many folders and files. I am not sure which is the main output file (and maybe some QC-related files).

Answer 1

[Jeremy Leipzig]

you might want to check out https://truwl.com/ - they have the official ENCODE ATAC-Seq pipeline as a runnable workflow