I am a beginner user in MOTHUR and my colleagues and I are trying to figure out how to deal with our sequences from bacterial V6 region.
We have aligned the sequences using MOTHUR but it returned a very strange alignment file, with no regular aligned sequence (they were all mixed up).
Therefore, we tried to align using RDP and it retrieved a good alignment. The problem is that it eliminated sequences that were not aligned but the file “groups” remained with those sequences. So my first question is whether you know how to remove those sequences from the group file.
My second question is if you know how to eliminate sequences that were aligned, but are in a wrong position? For instance, using summary.seqs is it possible to see where I can start cutting the sequences?
Another strategy that we used to get over the first problem: we used split.groups, aligned the 20 libraries separately, then we used list.seqs and tried to merge them into one. Unfortunately, the sequences from each library did not align to each other.
As you can see, we have tried many things, but obtained no results.