The whole enchilada

In this Jupyter notebook, I ran the bismark alignment on the full range of my samples. The .txt file output can be found here. The .bam files produced were several GBs! I saved them in this OWL folder. I also uploaded all .bam output from my file subsets here.

My next step is to run these samples through methylKit in R. I’m going to test this first with the subset data I have, then start plugging along on these large files.