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Old 05-22-2009, 10:52 AM   #1
AnamikaDarwin
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Location: Boston

Join Date: Nov 2008
Posts: 26
Question Run maq on solexa data with simulated qual scores

Hello,

I have single-end solexa reads, wherein the qual scores are the same for every base. I would like to be able to run maq map on this data. With the default options, I am not getting any alignments at all. Can anyone suggest what parameters I could possibly tweak?

Thanks,
Mika

Last edited by AnamikaDarwin; 05-22-2009 at 12:00 PM.
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