If you work with genome peaks, which are made after fastq files mapping and counting reads with peak detection tools you face a dilemma of annotating those peaks in for instance ChIPpeakAnno package using some included list of genome maps. Those maps can be close to the map you used for the fastq mapping, but not identical. Ideally I would do fastq mapping and peaks annotation with the same map. This is possible. Here I show how you do it within ChIPpeakAnno package using txdbmaker library.
#r #chippeakanno #txdbmaker #chipseq #atacseq #peaks #annotation
