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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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Many organizations study rare diseases, but few have a mission as impactful as Rady Children’s Institute for Genomic Medicine (RCIGM). “We are all about changing outcomes for children,” explained Dr. Stephen Kingsmore, President and CEO of the group. The institute’s initial goal was to provide rapid diagnoses for critically ill children and shorten their diagnostic odyssey, a term used to describe the long and arduous process it takes patients to obtain an accurate...12-16-2024, 07:57 AM -
Innovations in next-generation sequencing technologies and techniques are driving more precise and comprehensive exploration of complex biological systems. Current advancements include improved accessibility for long-read sequencing and significant progress in single-cell and 3D genomics. This article explores some of the most impactful developments in the field over the past year.
Long-Read Sequencing
Long-read sequencing has seen remarkable advancements,...12-02-2024, 01:49 PM
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