ChipSeq and DeepTools

Question

[qudrat.nii]

Hello,

I have done ChipSeq for a transcription factor and I am trying to generate a heatmap using deeptools. I am confused as to what bed file should I use for computematrix?

[ATpoint]

Peaks, genes of interest, random regions. The entire genome. Anything that fits your story.

[rfran010]

The bed file is whatever regions you want to look at. In your case, it may be the called TF peaks. Deeptools will then plot the signal (read counts) over each region (a line in the bed file) and present in a heatmap, where rows are the regions and color is the signal.