Note to self: Always double check things

• I forgot to change the code in my subset and full sample notebooks so that bismark_methylation_extractor ran on the files I produced instead of those in the dignore folder. I switched the code and everything still works!
• I thought I double checked what bismark_methylation_extractor outputs needed to be in the .gitignore but I left out several *deduplicated.txt files that were well over 100 MB. My mistake took me three days and one Github issue to figure out. Whoops. Now I know how to use the Github command line, add things to my .gitignore, and effectively undo commits to make Github Desktop happy.

I finished up the methylation extraction, HTML report, and summary report steps! I then started methylKit on the full samples to ensure reproducibility. When I’m finished, I’ll create BEDfiles and start to understand where differentially methylated loci are located and waht the gene functions are.