ChIP-seq Practice Exercises

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***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 called your eCommons ID within /n/scratch2/. Enter that directory and create a new directory called HCFC1_chipseq.

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c. Create a separate job submission script to run the shell script you created in b) on all four .fastq files. You have the option of running this in serial or parallel. Take a look at theautomation lesson to help with setting up the job submission script. 

d. Once the job submission script has finished running, use MACS2 to call peaks for each replicate using the input and treat BAM files and setting a q-value threshold of 0.05. How many peaks are being called for each replicate?

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