My lab recently switched from using 454 sequencing to using a Miseq platform. I was able to create a list file with both sets of sequences and I was hoping I could merge them at this point. The group files merge well but the list files do not when I use the Merge.files command. Is there a way to merge these files without going all the way back to the precluster step?
You really can’t merge list files since the only way to merge the OTUs would be based on their distance to each other. You really would have to go back to before align.seqs to merge these datasets. Also, unless you’re using the exact same primer set and sequencing the same bases, I’m not sure whether there is a reason to merge the datasets. There are just too many different biases involved. Why not analyze the datasets independently and then see where the analyses agree/disagree.