complex question cis-regulatory elements chip-seq

Question

[carlosalfonsogonzalez6]

Hi,

I have defined cis-regulatory elements by merging 4TF peaks of chip-seq experiments, I have identified the position of each motif in this cis-regulatory elements, I also have the same data for other 4 related species same coordinates obtained with liftover, so I want to compare like using some sort of alignment all the cis-regulatory elements and find the regions inside the cis-regulatory element that have lots of variation, the ones that have lower variation and intermediate and in which particular regions of the CRM (when I mean "variation" like more differences, at sequence level) for then annotate if there's gain or loss of transcription bindings sites.

I have tried doing it with one, and manually identified these particular regions, but how would you do it genome wide?

Please help

Answer 1

[Devon Ryan]

I would suggest that you download a conservation track for your organism from UCSC. There are typically a couple of them, so choose the one with the set of organisms that makes the most sense for your purposes. That'll make calculating things genome-wide MUCH more tractable.

[carlosalfonsogonzalez6]

Thank you, Im have already done that, Im looking for something more specific