Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • TSS v/s peak fraction graph for ChIP-Seq

    Dear All,

    I want to plot a graph of TSS v/s peak fractions for my ChIP-Seq data. Organism :Rice.
    I have the peak files containing the TSS distances but not able to figure out how to plot the graph. Any help would be much appreciated.

    Thanks in anticipation
    Kushal

  • #2
    Are you trying to do a density plot? This shall be very easy to do in R. You can even use Excel I guess.

    If you are trying to draw a TSS plot for short read coverage, you can use ngs.plot. It is a very powerful tool for this kind of tasks.

    Comment


    • #3
      Thanks buddy. I was more concerned about the peak fraction. Well, will try ngs.plot and get back.

      Many thanks
      Kushal

      Comment


      • #4
        Do you want to overlap the peaks with the TSS region to see how many peaks are at TSS (-3kb to TSS)?
        Bedtools or Galaxy can do this kind of job.

        Comment


        • #5
          I apparently have to use "kolmogorov smirnov" test to obtain this plot. But have no clue how to go about it.

          Kushal

          Comment

          Latest Articles

          Collapse

          • seqadmin
            The Impact of AI in Genomic Medicine
            by seqadmin



            Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
            02-26-2024, 02:07 PM
          • seqadmin
            Multiomics Techniques Advancing Disease Research
            by seqadmin


            New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

            A major leap in the field has
            ...
            02-08-2024, 06:33 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 06:12 AM
          0 responses
          20 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-23-2024, 04:11 PM
          0 responses
          67 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-21-2024, 08:52 AM
          0 responses
          75 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 02-20-2024, 08:57 AM
          0 responses
          66 views
          0 likes
          Last Post seqadmin  
          Working...
          X