I know the questions seem naive (I am working on slurm environment):
- What command should I use to run the ENCODE ATAC seq pipeline?
- 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).