ChIP-seq peaks annotation

Question

[Maurice]

Hi everyone,

I have a set of ChIP-seq peaks that have been annotated to my reference genome. To annotate the peaks, I have assigned a peak to a gene if the distance between the peak's start and gene's start is the shortest. However, in some cases, I found peaks that clearly falls within a gene but that have been assigned to the previous gene and that has been annotated as uspstream of that gene.

How can I fix this issue? I have used ChIPpeakAnno to perform the annotation.

Thanks to everyone that will help

Answer 1

[zau saa]

How about trying ChIPseeker?