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05-15-2013, 11:31 AM
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#1 |
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Member
Location: philadelphia Join Date: Aug 2012
Posts: 13
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novoalign mapping
Hi,
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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