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Update - 2-23-15

Update - 2-23-15

Mar 02, 2015
Update 2/23/15:

I have re-worked my concept map to more accurately reflect the necessary steps in the analysis as I understand them. I'm still finding software for determining hypermethylated regions. I will update this map soon once I'm finished figuring that out.

Other info: I checked the Discovery Environment in iPlant and programs for working with bisulfite sequencing data are not yet implemented. So, I will be planning on using the UA HPC for this. Hopefully this will work, as my computer is pretty decent, but the HPC is surely a better solution and it will probably run these scripts in a much shorter amount of time.

To-do:

  1. Get HPC access, determine if available storage space is enough for this project.
  2. Download A thaliana genome, download Bis-seq data.
  3. Try using Bowtie + Bismark to understand its output.