For a while we have been using 7 mer barcodes, but have recently changed to 10 mers. Can anyone see any problems that using a mix of mers in one run might cause?
We do 16s Sequencing on 454, trim at 350 bp, have a modified AmpliconNoise style de-noising pipeline and use qiime for taxonomy assignment.
both 7 mers and 10 mers work fine on their own.
The 7 mers are not suffixes or prefixes of the 10 mers.
Anyone ever done this? I cant think of any obvious problems, but would love some reassurance. I am thinking possible specificity issues with higher lengths or bioinformatic hiccups ?