Peaks annotation on bacterial genome

Question

[Maurice]

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.

Answer 1

[acvill]

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

Answer 2

[Maurice]

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