I have a very basic question about using deeptools computeMatrix function to plot ChIP/ATAC-seq signal across TSS sites. I am just curious what is the ‘standard’ way of making the bed file of the TSSs I want to plot. I can make the bed file in two ways:
I get the gene start coordinate of my genes of interest from an online database like ensemble and make the bed file. This gives me one start site per gene.
I get all ensemble annotated TSSs associated with a gene which gives me multiple regions associated with each gene. This seems like the better option as I am not ignoring any TSS but I am concerned that since most TSS are pretty close to each other I will be double counting most of them.
Since such plots are very common in literature, I was just curious what is the best practice for making them?