Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Problem with visualizing Chip-Seq peaks

    Hi there,

    I am having trouble to visualize my Chip-Seq peaks called by MACS in two subsequent biological replicates.
    I let MACS generate wiggle files of the peaks that I could use individually for visualization, but ideally I would like to look at only the peaks that have been found in both replicates and throw out anything that is only found in one of them.

    So, I took the bed files generated by MACS, concateneated them and clustered any regions overlapping by 1 bp from both replicates into 1 region which should give me only the peaks found in both replicates.

    However, when I load the bed files into my prefered genome browser (zenbu), for each peak I can only get (as opposed to the wig files) a bar that covers the region, but no quantity of tags or signal or whatever.

    So how do people show those beautiful peaks in all the papers that have those nice peak shapes? What kind of file should be used for that?

    Thank you very much for your help!
    Cheers,
    Tobias

Latest Articles

Collapse

  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    Yesterday, 07:01 AM
  • seqadmin
    Current Approaches to Protein Sequencing
    by seqadmin


    Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
    04-04-2024, 04:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 04-11-2024, 12:08 PM
0 responses
57 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 10:19 PM
0 responses
53 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-10-2024, 09:21 AM
0 responses
45 views
0 likes
Last Post seqadmin  
Started by seqadmin, 04-04-2024, 09:00 AM
0 responses
55 views
0 likes
Last Post seqadmin  
Working...
X