Annotation of 100kb region in genome
I have a question. I had been analyzing DNA-sequencing data with the sliding window of 100kb. I found certain regions to be enriched in the sliding window of treated sample in comparison to control region. I annotated those regions using ChIPpeakAnno: a Bioconductor package to annotate. After annotation I would like to know what percentage of the region are associated with promoter, intergenic, intronic and 3 UTR and 5'UTR. Is there any tool to annotate it? I did try to use CHIPseeker but it did not give right conclusion. Is there any alternative tool or if I could direct the bed file from UCSC browser and with this information and intersect with my bed file.
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