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12-28-2008, 11:33 AM
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Junior Member
Location: Copenhagen Join Date: Dec 2008
Posts: 3
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MAQ: finding the stop position of an alignment
Hi
I am using MAQ and have a short alignment question. For each aligned sequence I want to find the start and stop position of the reference sequence. The start position is given by MAQ and the stop position is start+ total alignment length. So is the total alignment length the same as the "length of the read" (output from MAQ) and does that value include gaps/insertions introduced by MAQ-aligment? |
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