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Need A Recommendation For A Package Or A Method To Detect Chip-Seq Enrichment Around Binding Sites

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

r wiggle perl
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updated by Neilfws Neilfws • written by thefirmament0 • thefirmament0

2 answers

  • 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.

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written by Ido Tamir Ido Tamir

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

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written by Anthony Mathelier Anthony Mathelier

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