Multiplexing vs single plexing

[Dolphin22]

Hey guys

I have a question on multiplexing libraries:

1) When is it useful to do multiplexing and when should you do one library per lane?

2) What are the advantages/disadvantages of multiplexing?

[GenoMax]

You are guaranteed a certain number of reads from a lane of (illumina) flowcell (long as other experimental variables (specially quality of libraries) are normal).

Depending on what experimental question you are trying to answer you may not need that many reads for a single sample. This fact coupled with the a need to run multiple samples would be a good candidate for multiplexing your samples.

Additional effort would of course be needed to make the multiplex libraries. You would also need to titrate your libraries so that you will be guaranteed to get a reasonable proportion of reads after demultiplexing.

There are experimental designs that deliberately use multiplexing (even when one may need a full lane of sequence per sample) where one would pool multiple samples and then run the pool on all 8 lanes on one or more flowcells. This way you can avoid lane/flowcell effects (and the possibility of failure of one or more lanes on some runs).

[pardhu]

can anyone plz advise me what are the adapter indexes are best for 4 plexing?