Creating heatmap for ChIP-seq using deeptools

Question

[biology_inform]

Hi all,

I am a newbie in ChIP-seq, and I conducted my analysis using the nfcore ChIPseq pipeline. After reviewing the results, I now need to perform more specific analyses. With nfcore, I generated informative heatmaps that provide a general overview of my ChIP-seq data (I will upload the heatmap).

My first question is: Based on my readings, I understand that this heatmap illustrates the general profile of ChIP-seq using the entire genome. If this is not the case, could someone please clarify?

Now, for my second question: I have three specific genes, and I would like to create a heatmap for these genes, including their 1.5kb upstream and downstream regions.

To do this I am planning to do these followings;

• I will use computeMatrix function of deeptools

computeMatrix reference-point  \ 
            --referencePoint TSS \ 
            -b 1500 -a 1500 \ # define the region you are interested in
            -R ./3genes.bed \
            -S ./mybigwig.bigwig  \
           --skipZeros \
            -o output.gz \ # to be used with plotHeatmap and plotProfile

I will use the provided code to generate a matrix necessary for creating the heatmap. To generate a gene-specific heatmap, should I create a separate matrix for each gene?

I intend to create a heatmap specific to one gene. If you have any additional recommendations, I would appreciate your input.

I have attempted to explain my question to the best of my ability. If additional details are required, I am more than willing to provide them.

Thanks.