Question: Annotation File for Enchancer Regions in Ensembl mm10 genome
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gravatar for hkarakurt
2.4 years ago by
hkarakurt100
hkarakurt100 wrote:

Hello everyone, I analyzed a ChIP-Seq Data (H3K4me1 and H3K27ac) and I need an enhancer annotation file (GFF/GTF) to use in SeqMonk. Is there any annotation file for enhancers?

Thank you.

chip-seq enhancer • 627 views
ADD COMMENTlink written 2.4 years ago by hkarakurt100

Enhancers are highly cell type specific regulatory elements. No, there is no simple consensus list that you can download. But as you have ChIP-seq data, you could use MACS2 to call peaks for both datasets and take the intersect as putative enhancer regions. This you then can write into the GFF format.

ADD REPLYlink written 2.4 years ago by ATpoint41k
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