Data that is uniquely aligned to a genome could be viewed as a custom track in the UCSC genome browser (viewable only from the machine it was uploaded). More on UCSC custom tracks athttp://genome.ucsc.edu/goldenPath/help/customTrack.html. To generate a track in the BED format from Gerald *_realign.txt files (let's say for lane 3, assuming 25 nt sequences):
cat s_3_????_realign.txt|egrep -v '^#'|perl -ane 'if (@F>3){$_=~/(chr.+):(\d+)\s([F|R])/;print $1,"\t",$2,"\t",($2+25),"\n"}'> s3_customTrack.txt