ChIP-seq Practice Exercises

***NOTE: When working on O2, be sure to run this in /n/scratch2/ rather than your home directory .****

# ChIP-Seq Analysis Workflow

1.  Create a directory on /n/scratch2 using your eCommons user ID as the directory name. Within that directory create a directory called HCFC1_chipseq.

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OPTIONAL: If you feel very ambitious get X11 setup on your personal account and try running ChIPQC to create a report for HCFC1.Discuss the quality of the data using these metrics. 

     X11 setup instructions are on this page under the "SSH X11 Forwarding" subheader. If you run into problems here please reach out to HMSRC folks, this is known to be tricky!

g. Sort each of the narrowPeak files using:

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