Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • chip-seq data analysis with galaxy

    Hi all! I am very new to this field, so I apologize in advance for my ignorance. I have done several chip-seq experiments on a protein from A.thaliana that functions in homologous recombination. I am struggling a lot with analyzing my data, mostly because I do not completely understand how the tools work. I use galaxy to do the analysis, Bowtie and MACS.

    I have several questions regarding these tools, hopefully someone will help!
    1. I know MACS provides the peak scores as -10log(pvalue) and it gives me ranges usually from 50-3100. But how does MACS2 calculate the score? Using the same dataset, I get very narrow ranges usually in single digits.
    2. What do treatment wig and control wig files show? I read that they show the binding signal, however this explanation is way to vague for me. And how can I correlate the peak bed file to the bigwig file on a genome browser?
    3. When I use MACS to call the peaks, I use default setting (pvalue cutoff 1e-5, and MFOLD value of 32). However, MACS fails everytime since it cannot find enough paired peaks to build the shifting model. Lowering the MFOLD value does not help. Only when I choose not to build the shifting model, only then will MACS succeed in calling the peaks. But, now I am worried, can I trust these peaks that MACS called? If it cannot make a shifting model, how could I predict the location of the binding site? I leave the arbitrary shift size 100 bp, but how do I know if this is the proper value to use? I also read that MACS cannot build the shifting model since there is no defined peaks, this can be a result of broad peaks (like for RNApol), it looks like my peaks are broad as well.

    Thank you for your help!!!!

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