I am utilizing the nf-core/chipseq pipeline (https://nf-co.re/chipseq/2.0.0) for ChIP-seq of analysis (H3K27ac and H3K9me3) with a focus on identifying peaks associated with transposable elements. Any advice on potential modifications within the nf-core/chipseq pipeline to effectively handle these multimapped reads during both the mapping and peak calling stages. I could see this pipeline retains multimapped reads via multiple aligner options like BWA, Bowtie2, STAR at mapping stage by default [--keep_multi_map] Does the nf-core/chipseq pipeline support any peak callers that are better suited for handling multimapped reads? Or Are there recommended modifications in MACS2 o within the pipeline to accommodate the analysis of TEs