questions about the annotation results from ChIPseeker.

[xuxuefen007]

I don't understand the annotation results from ChIPseeker. Theoretically, all the peak information contained in the peak file should be retained in the output of annotatePeak. The position and strand information of the nearest genes are reported, and the distance from the peak to the TSS of its nearest gene is also provided. However, in my results, the geneChr and the chromosome in the first column (peak chromosome) don't match. Does this mean that the peak is being associated with genes on a different chromosome?

Since my results show many such cases where the peak is associated with genes from different chromosomes, I am having trouble understanding why this is happening. I also found similar results on Galaxy (i.e., the peak chromosome and geneChr don't match). You can see this issue by checking the link below and scrolling to the bottom of the results:

https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=376f7eb7122465c4&tool_config=%2Fsrv%2Ftoolshed-repos%2Fmain%2F003%2Frepo_3935%2Fchipseeker.xml&changeset_revision=8bd92f2404dd&render_repository_actions_for=tool_shed

Can you explain why this happens? Thank you.