I have a problem, working with fungi and ITS sequences. I have followed part of the SOP and have an unique fasta, unique name and a group file. I then did CD-hit to cluster the unique fasta sequences, and then manually edited these clusters so that I have a list file in the same format as an example I found. Then I would like to do make.shared with the list and group file, but get errors about “xxx is in your group file and not your list file”. I understand that is because I used uniqe sequences to make the list file.
Question is. Is there a way around this problem, or do I have to work on all sequences when clustering using CD-hit? I have around 250000 of them, and hope to avoid this. Think there would be some difficulties when manually making the list file then.