HiSeq MiSeq library compatibility ?

[subxero]

I am looking to run some libraries I initially prepped for HiSeq via Trueseq RNA V2 on the MiSeq and have a question.

So I have read that the protocols are compatible, but the MiSeq only does PE reads and because of this your adapters need to be complimentary?

I am not sure exactly what this means? And where in the library prep I would have to make note of this? Or is all the PE SE stuff determined later in the clustering and the Single Index libraries I prepped should be good to go for the MiSeq because I will cluster on the MiSeq so all should be well?

[mcnelson.phd]

Pretty much any library that can work on a HiSeq will work on the MiSeq, with the only exceptions being some of the old discontinued TruSeq kits.

Also, the MiSeq can do single ends reads, it's just not the common workflow. All you have to do is set up the sample sheet correctly, which isn't too hard to do with Experiment Manger. You'll probably be wasting reagents since the kits are designed and have enough reagents primarily for paired end workflows, but that's not a big issue if your fine with it.