Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • suludana
    Member
    • May 2008
    • 61
    #1

    Chip-Seq Analisis

    I am analyzing my first data of Chip-Seq (with the antibody H4K16Ac) using Partek.

    In the initial step of detecting peaks I obtained a lot of peaks for some of the samples (100.000 – 200.000) and of course, then, I obtained large lists of associated genes. How can I do to filter these data? The control (not IP) is not enough to reduce substantially these values.

    Can I filter by the number of reads in each peak? In this case which would be the optimal value?

    Thanks!
    Tags: None
    • snetmcom
      Senior Member
      • Oct 2008
      • 159
      #2
      These are the same issues you get with every Chip seq experiment.
      Focus on a few genes and adjust some of the filters, then see how it plays with the rest of the data.

        Comment

        • suludana
          Member
          • May 2008
          • 61
          #3
          Do you think it would be correct to adjust filters based on some housekeeping genes?

            Comment

            Previous template Next

            Latest Articles

            Collapse
            • SEQadmin2
              Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
              by SEQadmin2



              Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

              Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating              ...
              10-14-2026, 09:55 AM
            • SEQadmin2
              New Genomics Technologies Take Aim at Long-Standing Limits
              by SEQadmin2


              Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

              We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing              ...
              09-28-2026, 10:25 AM
            View All

            ad_right_rmr

            Collapse

            News

            Collapse
            Topics Statistics Last Post
            Exeter-Led Study Maps What an Average Human Genome Looks Like by SEQadmin2
            Started by SEQadmin2, Yesterday, 11:13 AM
            0 responses
            18 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            Yesterday, 11:13 AM  
            Long-Read Sequencing Uncovers Cancer Mutations Conventional Testing Missed by SEQadmin2
            Started by SEQadmin2, Yesterday, 10:48 AM
            0 responses
            18 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            Yesterday, 10:48 AM  
            Mayo Clinic-Led Study Detects DNA Mutations Across Noncancerous Tissues by SEQadmin2
            Started by SEQadmin2, 10-15-2026, 10:52 AM
            0 responses
            36 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            10-15-2026, 10:52 AM  
            Study Finds Chromatin Motion Holds Steady Until Cells Face Stress by SEQadmin2
            Started by SEQadmin2, 10-14-2026, 05:39 AM
            0 responses
            42 views
            0 reactions
            		 Last Post SEQadmin2
            by SEQadmin2
            10-14-2026, 05:39 AM  
            View All
            Working...