We are in the planning phase for an experiment that requires sequencing of a DNA pool of length about 140bp. It is crucial that the entire fragment is sequenced. Platform will be Nextseq500 or MiSeq, depending on what the Power Analysis will demand as sufficient read depth for what we want to do. Anyway, I would like to ask for your advice on the running mode. Should we perform 150bp single-end or 2x75bp paired-end sequencing? I ask because typically base quality decreases towards the end 3' end. Is it therefore advisable to run it paired and then merge the two reads into a consensus sequence?
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Originally posted by atpoint View PostWe are in the planning phase for an experiment that requires sequencing of a DNA pool of length about 140bp. It is crucial that the entire fragment is sequenced. Platform will be Nextseq500 or MiSeq, depending on what the Power Analysis will demand as sufficient read depth for what we want to do. Anyway, I would like to ask for your advice on the running mode. Should we perform 150bp single-end or 2x75bp paired-end sequencing? I ask because typically base quality decreases towards the end 3' end. Is it therefore advisable to run it paired and then merge the two reads into a consensus sequence?
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