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Old 05-15-2013, 11:31 AM   #1
Location: philadelphia

Join Date: Aug 2012
Posts: 13
Default novoalign mapping

I want to use novoalign to map reads - allowing up to 15 mismatches for 100 bp paired-end reads

I am new to novoalign(went through the manual) and confused with some of the options like -t,-x,-r etc..

so for 15 mismatches i should give something like

-t 500

what would be -x then?

this is the command line i am thinking to run

novoalign -d genome -f A_1.fq A_2.fq -t 500 -r All -o SAM > out.sam

Is this correct?

thank you
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