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Old 02-04-2020, 03:28 PM   #4
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,076
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Does change of default index sequence lead to Miseq run or demultiplexing fail?
Demultiplexing may fail, if your indexes are non-standard and you provide standard indexes (but the run will not fail so don't worry). Edit the samplesheet and put the actual indexes you used. You should be able to demultiplex the data either locally on MiSeq or using standalone bcl2fastq. If you use the correct samplesheet when you start the run then everything should be fine.
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