Hi there, I'm trying to plot a metagene profile for a set of peaks. So far, I'm using makeMetaGeneProfile.pl (homer software) as follow:

makeMetaGeneProfile.pl rna hg38 -size 3000 -hist 10 -p mypeaks > metagene_profile_peaks_

and my peaks looks like this:

peaks_41    chr1    2124076 2124431 *
peaks_43    chr1    2155055 2155929 *
peaks_81    chr1    3605028 3605680 *
peaks_171   chr1    7147516 7147860 *

apparently the program works as it doesn't give me any error and generates the output, the problem is that all the values are zero, which makes me things something is going wrong.... any advice or idea? Maybe there is another software that I can use with bed files

PS. I've used computeMatrix from deeptools, which work incredible well if you have original bam files, but for this approach, I do not feel very confident neither.