Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • ChIP-seq peak caller that handles biological replicates

    Hi guys,

    I'm quite new to the field and trying to find my way around all available resources is a challenge so I'm asking for some advice here.

    I've preformed ChIP-seq for a transcription factor (thus expecting "narrow" peaks) in biological triplicates complete with input controls.

    To analyze my data I would like a peak caller that can make use of the biological replicates, is there one out there?

    I know I can run each replicate separate and overlap common peaks but if there is software that can make use of the replicates and turn it into statistics I'd prefer that option.

    Best regards,

    Anna

  • #2
    Originally posted by AnnaE View Post
    Hi guys,

    I'm quite new to the field and trying to find my way around all available resources is a challenge so I'm asking for some advice here.

    I've preformed ChIP-seq for a transcription factor (thus expecting "narrow" peaks) in biological triplicates complete with input controls.

    To analyze my data I would like a peak caller that can make use of the biological replicates, is there one out there?

    I know I can run each replicate separate and overlap common peaks but if there is software that can make use of the replicates and turn it into statistics I'd prefer that option.

    Best regards,

    Anna
    Hi Anna,

    It seems what you are looking at is something like the Bioconductor package DiffBind http://www.bioconductor.org/packages.../DiffBind.html

    So you your workflow could be:
    - For each library, align reads to your reference genome
    - Call peaks separately for each library (using he input control) using your favourite peak caller (e.g. macs)
    - Pass aligned reads (bam files) and peak sets to DiffBind for differential binding analysis making use of biological replicates

    Hope this is what you are after...

    All the best
    Dario

    Comment


    • #3
      i think CisGenome (www.biostat.jhsph.edu/~hji/cisgenome/) can do exactly what you want.

      Comment


      • #4
        Thanks for taking the time to answer, I appreciate it!

        @Mudshark: Thanks, that looks very interesting indeed. I'll be trying it out for sure!

        @dariober: At this stage I'm not looking for differential binding, I only have ChIP-seq from one condition so what I want is TF binding map so to speak.

        Best regards!
        Anna

        Comment


        • #5
          Originally posted by AnnaE View Post
          Thanks for taking the time to answer, I appreciate it!

          @Mudshark: Thanks, that looks very interesting indeed. I'll be trying it out for sure!

          @dariober: At this stage I'm not looking for differential binding, I only have ChIP-seq from one condition so what I want is TF binding map so to speak.

          Best regards!
          Anna
          diffbind was suggested because if you were to use something like macs to call peaks, it would not take biological replicates into consideration. after calling peaks in macs, you would use diffbind to perform the overlapping of the peaks to find peaks called in all biological replicates. similar work could also easily be done using bedtools intersect.

          edit: or just use cisgenome as was suggested.

          Comment


          • #6
            Hi,
            You can also try IDR:

            Access Google Sites with a personal Google account or Google Workspace account (for business use).


            Q

            Comment


            • #7
              Hi, for replicated ChIP-Seq data, you could try running PePr (https://ones.ccmb.med.umich.edu/wiki/PePr/).

              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
              8 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, Yesterday, 06:07 PM
              0 responses
              8 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
              66 views
              0 likes
              Last Post seqadmin  
              Working...
              X