Question: complex question cis-regulatory elements chip-seq
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gravatar for carlosalfonsogonzalez6
2.4 years ago by
carlosalfonsogonzalez610 wrote:

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

chip-seq • 761 views
ADD COMMENTlink modified 2.4 years ago by Devon Ryan95k • written 2.4 years ago by carlosalfonsogonzalez610
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gravatar for Devon Ryan
2.4 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k wrote:

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.

ADD COMMENTlink written 2.4 years ago by Devon Ryan95k

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

ADD REPLYlink written 2.4 years ago by carlosalfonsogonzalez610
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