Announcement

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

  • epigen
    replied
    MACS does not use any quality filters and if a read is mapped to different locations it will count it just as many times. It only removes reads that it considers to be duplicates (same start coordinate).
    Reads that map to multiple locations should have mapping quality 0, so you can throw them out using samtools view -q 1

    Leave a comment:


  • Rachelly
    started a topic ChIPseq question (MACS)

    ChIPseq question (MACS)

    Hi all,

    Does anyone knows if MACS uses the alignment quality score written in the SAM file, or does it use any alignment in the input SAM file?

    Also - How does it cope with a read that was mapped to different locations in the genome? Does it ignore it or randomly pick one location for it, as I heard other programs do?

    Thanks,
    Rachelly

Latest Articles

Collapse

  • 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
  • seqadmin
    The 3D Genome: New Technologies and Emerging Insights
    by seqadmin


    The study of three-dimensional (3D) genomics explores the spatial structure of genomes and their role in processes like gene expression and DNA replication. By employing innovative technologies, researchers can study these arrangements to discover their role in various biological processes. Scientists continue to find new ways in which the organization of DNA is involved in processes like development1 and disease2.

    Basic Organization and Structure
    Understanding...
    01-22-2024, 03:25 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 08:57 AM
0 responses
12 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-14-2024, 09:19 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-12-2024, 03:37 PM
0 responses
408 views
0 likes
Last Post seqadmin  
Started by seqadmin, 02-09-2024, 03:36 PM
0 responses
648 views
0 likes
Last Post seqadmin  
Working...
X