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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1. 1. 1. Run FASTQC 
      2. Align reads with Bowtie2 using the parameters we used in class.
         NOTE: For the Bowtie2 index you will need to point to the hg19 index files from: /n/groups/shared_databases/igenome/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/
      3. Change alignment file format from SAM to BAM (can be done using samtools or sambamba)
      4. Sort the BAM file by read coordinate locations (can be done using sambamba or with samtools)
      5. Filter to keep only uniquely mapping reads (this will also remove any unmapped reads and duplicates) using sambamba
         
      6. Index the final BAM file. This will be useful for visualization and QC.

**NOTE: The script will require positional parameters, and using basename will help with the naming of output files**

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