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Old 02-03-2020, 04:14 PM   #1
Tom2013
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Location: Canada

Join Date: Sep 2013
Posts: 19
Default Change standard index sequence in sample sheet for Miseq

We synthesized fusion primers (i.e p7(or p5)-index-Transposase- gene_specific_Primer) using the Nextera adapter and index sequences, and prepared a library for Miseq. When I prepared the sample sheet file for Miseq run, I noticed we used wrong sequence for only one index (N707): we used the reverse complementary sequence of N707 (the other index sequences are good).

Now, I may have two options to fix this:
1) use the default index sequences generated by the IEM software in the sample sheet; run Miseq as usual; most samples will be demultiplexed by the Miseq software except a few; then demultiplex the un-demultiplexed sequences for those samples that have used the N707 index.
I still need to figure out how to demultiplex the sequences.

2) After the sample sheet is generated, change the default N707 index sequence to the sequence that was actually synthesized, and then save the sample sheet for Miseq run. Will this work for Miseq software and sequencing?

I prefer option 2), but not sure whether the Miseq run will be successful. Any ideas will be much appreciated.
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