Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • plotting BSSeq Data

    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.

  • #2
    Have you looked at deepTools (https://deeptools.readthedocs.io/en/develop/ )?

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    9 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    49 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    67 views
    0 likes
    Last Post seqadmin  
    Working...
    X