Hi all, I'm trying to annotate peaks identified in ChIP-seq experiments in M. tuberculosis using ChIPpeakAnno on R. I would like to distinguish between peaks that are located in promoter regions or in coding regions. Is it that possible? Is there any code I could use to selectively distinguish between these two regions? Can I use a custom genome that includes also promoters in addition to CDS?
Thank you in advance for your help.
2 answers
You can call annoPeaks with a GRanges annotation object that includes promoters, then use assignChromosomeRegion to summarize peak distributions associated with different genome elements. See the manual:
assignChromosomeRegion
Summarize peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR
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