Question: Plotting MBD-seq results
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gravatar for BioinformaticsLad
23 months ago by
BioinformaticsLad160 wrote:

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.

enter image description here

mbd-seq methylation • 627 views
ADD COMMENTlink modified 23 months ago by cmdcolin1.5k • written 23 months ago by BioinformaticsLad160
4
gravatar for cmdcolin
23 months ago by
cmdcolin1.5k
United States
cmdcolin1.5k wrote:

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

ADD COMMENTlink modified 23 months ago • written 23 months ago by cmdcolin1.5k

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.

ADD REPLYlink written 23 months ago by BioinformaticsLad160
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