I am reanalysing a ChIP-seq dataset I downloaded from GEO. Using the nf-core ChIP-seq pipeline, I have performed QC, alligned reads and called peaks using MACS. I am now at the point where I have annotated peak files and bigwig files (which can be visualised in IGV) for each of my samples. Now, I'm a bit unsure how to proceed from this point. The specific question I would like to answer is; do my targets bind within the region of tRNA genes and how does this change with experimental treatment? I'm not interested in genome-wide binding of my targets; only within tRNA genes.
How would I go about answering this question? I have a tRNA genes bed file which I can visualise alongside my sample peaks and I can see that there are peaks within the tRNA genes but I'm confused as to how I quantify this binding/display this in terms of figures/plot.
Any help would be much appreciated!