Homer software to generate the TSS heatmap of specific gene list instead of all genes

Question

[spiritedaway89]

Hi,

My apology if this has been asked before. I am able to follow the Homer documentation and generate the heatmap using annotatePeak.pl. The command line is below.

annotatePeaks.pl <peak file> <genome> -size <num> -hist <num> -ghist -d <tag directory 1> [tag directory2] ... > <output matrix file>

I was able to get a nice heatmap after clustering and visualizing it.

However, the annotated peak file usually contains all the peak coordinates for all genes in my project, I am wondering if there is a way to filter the coordinates to TSS only and also filter the genes? Do I need to go in TSS mode, do FindPeak.pl again? My possible solution, I was able to manually edit the text file and remove the undesired genes and annotated peaks that are not TSS. I am hoping to have just one or two TSS per gene (one row in heatmap) and then generate the heatmap. Is this reasonable to do it?

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.