Plotting MBD-seq results
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2.3 years ago

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.

methylation mbd-seq • 762 views
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2.3 years ago
cmdcolin ★ 1.5k

The deepTools package can do things like this

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

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

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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.