Viewing sense and antisense alignment separately

[uqdbarr1]

I am new to the field and I am analysing small RNA reads from Illumina GAII. Currently I am using maq to align reads with genes of interest but I have had trouble batching the small RNAs that align to the gene in sense and antisense orientations separately. Is there a script I can use to take the .map output or pileup output from maq to display the sense and antisense alignments in separate graphs? Is there a software package that does this for me?

Sorry for the seemingly straightforward questions but I am doing my head in trying to find a solution that doesn't involve me learning perl or python and any help would be greatly appreciated.
[email protected]