Comparing ccans with chIP-seq data.

[nkleine...@gmail.com]

Hey everyone, 

I was wondering how one would compare ccans to chIP-seq. data (In my case H3K27ac). My plan is to compare co-accessible sites with potential enhancers. Is there a way to do that like in the vignette with the ChIa-PET data? Or does anyone have suggestion to do something comparable?

Best wishes and thanks in advance!

Niklas

[hpl...@gmail.com]

Hi Niklas,

You won't be able to do exactly the same comparison as ChIA-PET because you won't have pairs of data, but you can certainly do an overlap and look for enrichment or enhancers for example. Check out annotate_cds_by_site. This function will add a column to your pData table of the overlap between bed format-like data (your chip-seq peaks) with your accessible elements.

Hope this helps,

Hannah