Longest Indexing Read You've Done?

[uberfinch]

Hello,


I'm building my own libraries using my own reagents and the small RNA adapter sequences. I'd like to have a 12 or 15 bp-long indexing read. I wondered if people have experience with such long indexing reads--our Illumina rep says there is no reason it shouldn't work, but personal experience (in my own experience with these sequencers) is invaluable.

Cheers
Uber

[mcnelson.phd]

The Caporaso et al. method for doing 16S sequencing on the MiSeq uses a 12 base index, and we've never had any issues with doing that. You'll want to be very careful with your primer design if doing a custom indexing primer, but there's no reason why it won't work.

[Genohub]

Same here, I've done up to 12 base Illumina indices with no problem. Good thread describing how you can mix index lengths in the same run:

http://seqanswers.com/forums/showthread.php?t=32429&highlight=mixing+index

- Genohub