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

Question

[thefirmament0]

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

Answer 1

[Ido Tamir]

• 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.

Answer 2

[Anthony Mathelier]

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