Can I demultiplex data based on indexes in the forward primers if doing single-end sequencing?

Can I demultiplex sequenced data based on indexes on the forward primers if doing single end sequencing on HiSeq?

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I have prepared amplicon libraries using a different combination of forward and reverse primers. The forward and reverse primers used had different indexes, and I am planning to do 100bp single-end sequencing on a HiSeq lane .

My plan is to demultiplex HiSeq data based on barcode/index sequences on the forward primers, but the sequencing facility is saying that since there is no i7 index on the forward primer it is not going to work.

Please suggest.

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Thank you in advance for your help.


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Fuchsia Kelpieover 3 years ago

If you are using the NGS primers from the Joung Nat Protocol 2017 paper, then there are no barcode sequences on the forward primers, so you will not be able to demultiplex using the barcodes on the forward primer. The reverse primers should have barcodes that you can use for demultiplexing.

Crimson Lichover 3 years ago

Thank you very much for the information!

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