Hi, I am trying out mapping few million short reads(>5X coverage) using MAQ. I am trying to map the reads against hg18 ref genome. Now, the problem I face is that it gives me a lot of 'n' s in most part of my consensus sequence.
Something like
>chr1
aacgatagatacagatacACGATGCATGACagcatgcatgacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaagcaGTCAGTACGATCGACTAGCAaagctagatannnnnnnnnnnnnnnnnn
what should be the right command for MAQ to map amd asseble to get rid of the 'n's?
thanks
Something like
>chr1
aacgatagatacagatacACGATGCATGACagcatgcatgacnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaagcaGTCAGTACGATCGACTAGCAaagctagatannnnnnnnnnnnnnnnnn
what should be the right command for MAQ to map amd asseble to get rid of the 'n's?
thanks
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