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Session V: ChIP-seq and optional questions - Answer Key
****NOTE: The questions for Session V homework are more comprehensive to help you get a better feel for the workflow and will involve working with full datasets. Therefore, for this homework we suggest that you do not work in your home directory. Follow the instructions below to work on /n/scratch2.****
# 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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i. SUGGESTION: Use the resulting peaks from IDR to explore downstream tools for functional enrichment (GREAT) and motif discovery (MEME suite). Explain how these tools might help in drawing conclusions about your original hypothesis.
## OPTIONAL:
3. Use the full dataset available at /groups/hbctraining/ngs-data-analysis2016/rnaseq/full_dataset/ to perform the MOV10 analysis as listed below. Please make sure your working directory is NOT your home directory, and that it is in the group directory for your lab.
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