Good morning to everyone, I'm a student from Italy. In my epigenetics course I' had an assignment where I had to align reads obtained from BS seq of an arabidopsis thaliana toy genome, align the reads to a reference and do a methylation call using Bismark. I'd obtained a methylome data called "CX_context" that is like this:
(1.6 gb txt file). Using this data from CX_context, my teacher told me to plot a graph of the methylation level along the chromosome like this:
The hints that he gave to me were to use R studio, and search for an package that can do the "smoothing " on my data.
The question is... How can I check the methylation level if the methylation is a binary variable (methylated or unmethylated)? There's a package/tool that you can suggest me to use?
To do all these analysis we connetct via SSH to a linux based server.
Thanks to everyone that could help me.