I want to use findMotifsGenome.pl program in Homer to identify enriched motif in the aggregated regions from single-cell ATAC-seq data.
I wonder what the -size parameter means? In their document, I found two explanations: 1. length of sequences used 2. -size <#> (fragment size to use for motif finding, default=200); -size <#,#> (i.e. -size -100,50 will get sequences from -100 to +50 relative from center); -size given (uses the exact regions you give it)
Does it mean to 1)specify the sub-size within the given peaks, or 2)the DNA size in the prepared library fragment? I am more lean to (1). Then if I give (-100, 50), does it will only search for motif within this range in each of the peak given in the bed file? Note that the bed file I input has average peak size of ~1500. I am not sure whether 150 window is too small.
Also, does anyone knows the publication link to Homer? Could you post a link here if there is any paper I can read?