Peaks annotation on bacterial genome
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12 months ago
Maurice • 0

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.

ChIPpeakAnno annotation bacteria • 594 views
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Entering edit mode
12 months ago
acvill ▴ 340

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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12 months ago
Maurice • 0

Thank you for your kind reply! I have just a further question. Which is the difference between using annoPeaks and annotatePeaksinbatch with ChipPeakAnno?

Thank you for your help

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