I have the 3 IP (TF1, TF2, TF3) data, and I use mac2 callpeak to get the peak files (TF1.peak). I want to get the multiplot fig about three IP signals at 1, TF1 peak region 2, these IP singals at genes nearest to TF1 peaks . I am not sure what genelist file I should put in the config file? I tried to take first 3 columns from TF1.peak file and save as bed fie, but it did not work.
ngs.plot.r -G hg19 -R tss -C config6.txt -O epak.tss -D ensembl -FL 300
TF1.dd.bam TF1.bed "TF1" TF2.dd.bam TF1.bed "TF2"
Can anyone please give me some suggestions? Thanks very much for your great help.