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Old 06-22-2011, 09:00 AM   #3
jjpurwar
Junior Member
 
Location: Salt Lake City

Join Date: Jun 2011
Posts: 9
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Hi, so I did specify the --solexa1.3-quals as my option. I dont take for granted the default option.
I did check with tophat regarding this matter - turns out that they dont take mapping qualities into account. This is worrisome - since you might want to throw out poor quality alignments. But I guess thats the trade off since tophat is a really fast aligner....
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