Completed

Completed Items:

1. Data has been acquired: reference genome, BS-seq reads.
2. All data is now on the iPlant data store.
3. Bismark is installed on my home computer for testing purposes.
4. Verified that I can run the programs on my computer to generate a test output file to use for small-scale scripting tests.
5. HPC access is working.
6. Began preparing my reference genome for use with Bismark.
7. Bismark genome preparation, read mapping, and methylation extractor have all been run though iPlant.
8. Installed Methylkit, an R package that allows one to find differentially methylated regions and work with all sequence contexts.
9. Sorted my Bismark Outputs (.sam) for use with Methylkit
10. Shell script to sort my methylation status summaries.
11. Finished sorting my Bismark Methylation Extractor outputs (.txt summaries for sequence context specific methylation calls)
12. Wrote all the commands I'll need to use in methylKit
13. Wrote and tested python script for CoGe-import of Bismark data
14. Processed all methylation extractor files to be imported into CoGe