Question: Need A Recommendation For A Package Or A Method To Detect Chip-Seq Enrichment Around Binding Sites
1
gravatar for thefirmament0
6.0 years ago by
thefirmament020 wrote:

I have a downloaded chiq-seq wig file and a list of binding sites got from experiment. Now I want to get enrichment signal around our binding sites within 500bp. Is there any good package or methods for this work? Thank you in advance

perl R wiggle • 1.6k views
ADD COMMENTlink modified 5.6 years ago by Neilfws48k • written 6.0 years ago by thefirmament020
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gravatar for Ido Tamir
6.0 years ago by
Ido Tamir4.9k
Austria
Ido Tamir4.9k wrote:
  • CEAS does something like that for the command line and works with wig files - but might need equidistant sampling points in the wig file(?).
  • for a GUI usage I would use seqMiner. It also clusters your profiles, is very performant and easy to use, but its not open source and requires bed or bam file (not wig files). But its from all possibilities I think the best and quickest to work with if you have the bed files.
  • roll your own with bioconductors GenomicRanges or e.g. TransView

I would however recommend getting a hand on the original bed or bam file and working from there.

ADD COMMENTlink written 6.0 years ago by Ido Tamir4.9k
0
gravatar for Anthony Mathelier
6.0 years ago by
University of Oslo, Oslo, Norway
Anthony Mathelier870 wrote:

To look for overrepresented motifs in the vincinity of your binding sites, you should have a look at MEME, RSAT, and cErmit.

ADD COMMENTlink written 6.0 years ago by Anthony Mathelier870
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