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Old 03-09-2010, 02:20 AM   #1
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Default Mapping SOliD reads to a Newbler 454 alignment to correct errors

I have a 454 assembly from Newbler, which I know has frameshifts/unexpected stop codons in the middle of ORF's.

I would like to use a SOLiD run (which gives me 150x + coverage over the Newbler contigs) in order to correct for potential errors.

I've been using MAQ successfully to map the SOLiD reads to the Newbler contigs. However I can't see the correct - if there is one - method to extract a sequence that represents the 'overloading' of the SOLiD data. I'm using the 454 contigs as a scaffold, but I would like to extract the 'best possible' sequence over the scaffold from only the SOLiD reads.

Is there any way to do this in MAQ or in another package?
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