Michaela: Yes. Bowtie and BWA mappers will align illumina reads against a reference genome. Take a look at our quickie #7 at http://usegalaxy.org Thanks, anton galaxy team On Jan 15, 2010, at 3:11 PM, Michaela Lee wrote:

Hello,

I was wondering if Galaxy can align Solexa reads to a reference sequence. If not, can I upload my alignment data from Maq onto Galaxy and somehow work with that data online? Also, can Galaxy tell me which parts of the reference sequence have no reads aligned to them? I am basically trying to figure out which parts were not sequenced and compare those sequences between different subjects.

Thanks for your help.

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Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org