Hi, I have some ATAC seq data along with RNA seq data. I have generated bed files of common peaks and unregulated peaks between two cell types. I was using homer to find common and upregulated motifs which have mapped upregulated genes from one cell type to another. I read the tutorial of Homer. It says that find motifgenome.pl aims at finding differential motifs compared to the background. But there was just one peak file in the script so I am not sure what the background is. Is it just the whole genome (hg19) or what ? Is it ok to use findmotifgenome. pl to find the common motifs?
Homer generates a background set of sequences based on the characteristics of the peaks you supplied (size, GC, etc).
As to finding common motifs, I'm not entirely sure what you mean... Common motifs between what exactly? A little info about your expt design and data will help with the second part of your question.
And another problems is that even though I can generate the motif files that have common motifs with possibly targeted up-regulated genes but when I used annotatePeaks.pl to find whether specific motifs are in those common peaks with targeted genes which are unregulated, the generated files are weird. Firstly, the peak score are very high and the row which supposed to show Focus Ratio/Region Size is the gene names rather than NA like the normal format. How can I fix that or are there any other ways that I can reach what I want to do ?