Tom - the MiSeq moves your sample from the cartridge to teh flowcell through non-disposable tubing, there is a risk some carry-over will happen but this can be mitigated against with several relatively small changes.
Many applications will be largely unaffected, amplicons in heterogenous samples are likely to suffer the most.
Send your samples with different barcodes each time if you can.
Make sure to ask your facility to perform the washes between runs.
There is a hack to fool the MiSeq into thinking it is clean, don't use it! A maintensance wash is a bit of a pain but we'll be running them until this is fixed.
Many applications will be largely unaffected, amplicons in heterogenous samples are likely to suffer the most.
Send your samples with different barcodes each time if you can.
Make sure to ask your facility to perform the washes between runs.
There is a hack to fool the MiSeq into thinking it is clean, don't use it! A maintensance wash is a bit of a pain but we'll be running them until this is fixed.
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