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Help me understand MAQ indexing
Can anyone please help me clarify the following? Sorry if it is a dumb question!
I am reading the Methods' section of Maq paper.
If the first 28bp are indexed using the 6 templates, each read is "divided" into 4 sections (S1, S2, S3, S4) and the templates are 1100 , 0011, 1010, 0101, 0110, 1001. When the first template is applied, only the first two section S1 and S2 are considered. Now if during search I get a match with a read, that means that I have a perfect match on the first two sections (S1, S2) and I could have mismatches on the other two (S3, S4).
I don't see how this would guarantee up to two mismatches only, sicne I could have many mismatches in those sections that I am not considering.
What I am missing?
I am reading the Methods' section of Maq paper.
If the first 28bp are indexed using the 6 templates, each read is "divided" into 4 sections (S1, S2, S3, S4) and the templates are 1100 , 0011, 1010, 0101, 0110, 1001. When the first template is applied, only the first two section S1 and S2 are considered. Now if during search I get a match with a read, that means that I have a perfect match on the first two sections (S1, S2) and I could have mismatches on the other two (S3, S4).
I don't see how this would guarantee up to two mismatches only, sicne I could have many mismatches in those sections that I am not considering.
What I am missing?