Starting from fastq files (solexa s_n_sequence.txt files), it's easy to strip the barcode off the 5' end using fastx tools as follows:

cat ../6228VAAXX/s_6_sequence.txt | fastx_barcode_splitter.pl --bcfile barcodes.txt --bol --prefix s_6_ --suffix ".txt"

Then you can run the resulting files through bowtie to align them:

# run bowtie, -t is print time
# -k 1 match
bowtie -t s_cerevisiae -k 1 --best --solexa-quals s_6_A1.txt --sam | samtools view -S -b -o s6_A1.bam -