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I am interested to know what programs people use to plot CpG methylation data to create those pretty visuals you find in publications. I don't have any issues doing the analysis and identifying differential methylated sites and regions. However, I would like to be able to plot the average methylation of groups/samples across a chromosome. It seems that some type of smoothing is necessary because if you just plot all the points and connect them it is way to dense to plot with any program I can find. I am aware there is a program called BSSmooth but I really don't need to re-analyze my data, only plot it. I have searched and searched and just cannot find a program that was meant for this type of thing. A lot of people seem to use circos plot programs in R but I cannot figure those things out and I have yet to find any kind of tutorial on plotting methylation. I know it seems unimportant because it's really the differential methylation stats you want, but my boss always wants to "see" what the methylation looks like. Maybe people are just writing there own scripts using R. I am not at all good with plotting in R but can follow a tutorial. I have WGBS data and targeted BS data sets I would like to be able to visualize. Any suggestions would be greatly appreciated.
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Have you looked at deepTools (https://deeptools.readthedocs.io/en/develop/ )?
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The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...05-06-2024, 07:48 AM -
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...04-22-2024, 07:01 AM
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