Plotting MBD-seq results

Question

[BioinformaticsLad]

Does anyone know of any programs or R packages to plot MBD-seq methylation status results like this? Thanks!

I'm using the R package MEDIPS for my analysis.

Answer 1

[cmdcolin]

The deepTools package can do things like this

https://deeptools.readthedocs.io/en/develop/content/tools/plotProfile.html

You would prepare coverage files in the form of bigwigs with computeMatrix

https://deeptools.readthedocs.io/en/develop/content/tools/computeMatrix.html\

Converting aligned reads to bigwig is generally done from things like macs, which automatically makes wig files, or bedtools genomecov which creates a bedgraph file from a inputted bam, and then run bedGraphToBigWig

[BioinformaticsLad]

Very helpful, thanks! I wonder if you'd also know what package to use for performing GO annotations on MEDIPS results? I'd like to do GO annotations so I can visualize the results with clusterProfiler.