Previously took the analysis just through the mapping, but didn’t realize Steven wanted me to fully process the data.

So, as en exercise, I followed through with deduplication and sorting of the BAM files.

Then, ran a quick analysis using MethylKit in R. The analysis simply copied what Steven had done with another data set and I haven’t examined it very thoroughly, so am not well-versed on what it’s doing and/or why.

Jupyter Notebook (GitHub):

• 20180530_emu_oly_methylation_mapping_deduplication.ipynb

R Studio Project (download the folder, load project in R Studio, and then run the script in the scripts subdirectory to run the analysis):

• 20180531_oly_methylkit/

Will take the full data sets through this whole pipeline.