FindPeaks
This allows the user to prepend a string to chromosome names in the Wig files generated. If your reference genome files are labeled as 1.fa, 2.fa, etc, then you will need to prepend the string chr for the chromosome name to be recognized by the UCSC Genome Browser.

What it does

runs FINDPEAKS (http://sourceforge.net/apps/mediawiki/vancouvershortr/)