I'm trying to find the frequency of UA dinucleotide in a bed file. I want to convert the bed file to FASTA, count all the UA dinucleotides up, then divide by the total length of the FASTA file. Also, I probably need to compare the value I get above to the background, but I'm not sure how to go about this?

I understand HOMER might be able to help me?

I understand homer should do the counting for me and also create a background distribution for me. It looks like I need to build a basic motif file and give homer a bedfile of locations and motif file to find. However, I'm unsure of how to set this up.

Other suggestions are welcome.