multiplexing - how to choose adapter combinations

[pari.takle]

Hello everyone

I am new to NGS. Currently, I am trying to prepare MethylC-seq libraries. How do I choose adapters for multiplexing? I read blog on multiplexing on Bioo Scientific but still have doubts. Perhaps someone here can help ...

1. How do I choose adapter index for multiplexing? - there should be equal balance of red and green but how do I choose adapter combination that will work-
Will combination of CTAGCT and GCGCTA work?

2. If base in position 1 in adapter 1 result in signal in red channel, does base in position 1 in adapter 2 need to result in green channel or can be red?

Look forward to your comments!
Cheers

[nucacidhunter]

Your selected index sequences are good. Most kits will have instructions for multiplexing various number of libraries with different indices. Colour and base balance in each position is important to obtain maximum number of correctly demultiplexed reads but it does not need to be a perfect balance.

[pari.takle]

Thanks Nucacidhunter! At the moment I am using NEXTflex illumine compatible adapters from Bioo Scientific. (Unfortunately kit didn't come with instructions on multiplexing different indices)

Color and base balance in each position is important, does that mean if position 2 corresponds to red in adapter 1 then one has to choose adapter 2 such that position 2 in adapter 2 corresponds to green and vice-versa?

[nucacidhunter]

All NEXTflex DNA barcode manuals has recommendations for low level multiplexing options.