I first got about 120 .sff files from the company, which did the 454 analysis for us. :shock:
In the end we managed to merge them into 2 separate sff-file, but not one.
This is because they re-used the same bar-codes on two separate runs without any concern on how we designed the experiments.
I would like to follow the SOP, but I have some doubts how this segregation will effect the shhh.flows command etc.
If anyone has encountered a similar problem, I would really appreciate any suggestion how to handle it.
Thank you
Alex
If you want to keep the 2 runs separate, you should create a second oligos file. Then you can use the sff.multiple command, http://www.mothur.org/wiki/Sff.multiple, to run trim.flows, shhh.flows and trim.seqs. Something like:
You can create a design file, or use the get.groups and merge.groups commands if you would like to pool sequences from the same barcode and different runs later in your analysis.
