I would like to match (intersect) a quite big set of chip-seq peak bed files with a single bed file containing transcriptional start sites (TSS) identified by cage (cap analysis of gene expression). By using a large cohort of transcription factors (TFs), I am hoping to generate a map of the TFs associated with my promoters.
Technically, I have my promoter bed file and currently about 80 chip-seq peak bed files. I would like to look at TF binding in close upstream proximity of my promoters (for instance within 500 bp upstream of the TSS). I read that bedtools could be used for this, but I am limited to a windows laptop and I am unsure if this would work. However, I know a little but of R and would therefore prefer to use any R package that could the job.
I would be very grateful for any hints how I could start the analysis.
Thank you very much!