Manually creating list files

Hi all

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.

Erik Lysoe

Mothur is expecting the list file to contain all the sequences, not just the uniques. This is important since a unique sequence may represent multiple sequences from different groups and the make.shared command needs this information to get the correct abundances for each group for each otu.

Thank you!

I was afraid so. I thought there was a way, similar to “Phylotype”, where a name file and a taxonomy file give you a list file with all the sequences, not just the unique.