After viewing tutorials and reading the information associated with various 
tools, I ask that you point me toward an appropriate workflow for the following:

I sequenced (Illumina) 5 genomes of phenotype(+) samples and 1 genome of a 
phenotype(-) control. I uploaded fastqsanger files to Galaxy and performed 
Bowtie alignments. I want to find the allelic positions where the (+) genomes 
differ from the (-) genome.

Many thanks,


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