Has anyone looked systematically at the error rates in relation to Q values for the MiSeq (in particular when doing amplicon sequencing)?
We do amplicon sequencing 250bp paired end. Our findings are that the Q values and the error rate do not match. The error rate levels off at about 25. However, for certain positions in certain amplicons the rate of errors is even higher (see example).
We use Roche FastStart High Fidelity. It seems unlikely that that amount of errors is due to PCR artefacts?
Any idea how to deal with that? Anyone else has seen something like that?
We do amplicon sequencing 250bp paired end. Our findings are that the Q values and the error rate do not match. The error rate levels off at about 25. However, for certain positions in certain amplicons the rate of errors is even higher (see example).
We use Roche FastStart High Fidelity. It seems unlikely that that amount of errors is due to PCR artefacts?
Any idea how to deal with that? Anyone else has seen something like that?