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Old 03-25-2020, 10:23 AM   #5
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Location: Utah

Join Date: Mar 2010
Posts: 166

Originally Posted by GenoMax View Post
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.
This is probably a bit late for you, but I'll chime in here with my own experience for those who come after. I needed more indexes than were available in any Illumina product. However, rather than make up my own index sequences, I collected all of Illumina's 8 bp indexes, put them together into one list, eliminated any that were duplicates or too similar to others, and renamed them into one sequence. When I use those, I just make the sample sheet in Excel and import it into Local Run Manager to create a run. The system has no problem with nonstandard indexes, or with standard index sequences with a different name.
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