Kevin: Is this a diploid or haploid organism? anton galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org On Jul 12, 2011, at 11:38 PM, Kevin Pawlik PhD wrote:

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,

Kevin

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