I have performed ATAC-seq on two different biological samples. I want to compare peaks between these files, as well as enrichment for particular motifs.
Firstly, I have mapped my PE reads, and then removed duplicates. I now have a bam file, that I use deeptools BamCoverage to normalise to RPKM, and the output is bedgraph. I do these for both my samples that I wish to compare.
Now, I want to compare the motifs that are enriched in the peaks between the two files. Is the following a sound methodology:
- Run the resultant RPKM bedgraph files through Homer's findmotifsgenome.pl. Can the output knownResults.html and and homer de novo html, be compared between the two samples to check for differences in motif enrichment?