The MiSeq sample prep guide indicates that a seventh base is needed after the 6th base. What is the reason for that?
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Possibly because with the Illumina technology the accuracy of the base calling for any particular cycle (having to do with things like phasing/prephasing) depends partly on the next cycle, so I guess if you want to have 6-bases for the index read, you would actually do 7 cycles.
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Originally posted by GenoMax View Post@mastal is correct. Since phasing information can't be determined for the last base it is not used during (n-1 rule) downstream processing (demultiplexing).
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