Manually creating list files

Commands in mothur
1

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.

Thanks!
Erik Lysoe

2

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.

3

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.

Best
Erik