Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • mia2025
    replied
    My favorite tool for this kind of analysis is Diffbind. It requires peaks called for each individual replicate using the respective inputs and then generates a list of peaks which are statistically differentially bound (I believe it uses DESeq for this, but you can also switch to use EdgeR if you prefer). The good news is that the tutorial is very user-friendly and in depth and actually uses ERa ChiP Seq data from different cell types as a tutorial.

    Hope this helps

    DiffBind R Package : https://bioconductor.org/packages/re.../DiffBind.html

    Leave a comment:


  • ivan.costa@rwth-aachen.de
    replied
    One tool performing differential peak calling with replicates and supporting multiple input-DNA is THOR.

    Check here http://www.regulatory-genomics.org/THOR

    Leave a comment:


  • ShaunMahony
    replied
    I think that depends on what you are comparing. If you are comparing binding in different cell lines or in significantly different conditions, then you can indeed have sample-specific artifacts and ignoring the inputs will be the wrong thing to do.

    Shameless plug: Our MultiGPS software allows you to compare transcription factor binding across conditions in a principled way.

    Leave a comment:


  • Quantitative comparison between 2 IP ChIP-Seq samples, each with an input control.

    My initial question was how to quantitatively compare peaks from 2 ChIP samples, with accompanying inputs for each sample.
    macs2 bdgdiff allows one to take into account the inputs, but none of the other existing programs seem to allow this option.
    After doing research, the best option seems to just ignore the inputs, and compare the IP samples directly.

    According to the MMDiff authors:
    "Input correction is not necessary for differential peak calling as the local biases such as sequencing bias should affect all considered sample in the same way."
    Last edited by blancha; 06-13-2014, 06:05 PM. Reason: Deleted irrelevant post

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...
    Yesterday, 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, 02-23-2024, 04:11 PM
0 responses
39 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-21-2024, 08:52 AM
0 responses
57 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-20-2024, 08:57 AM
0 responses
42 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-14-2024, 09:19 AM
0 responses
65 views
0 likes
Last Post seqadmin  
Working...
X