Hi all,
I am working with LSU fungal sequences. I use Blast against an in-house database to classify the sequences and then create a .taxonomy file from the Blast output (long story but classify.seqs against my database puts the majority of my sequences in the unclassifed bin so I had to resort to Blast for classification and then come back to Mothur for making the shared file). Anywho, so I have that taxonomy file based on my Blast results which I then use in the phylotype command to create a .tx.list. All good so far. When I then use the .tx.list and the .count_table in the make.shared command, I get an error that there are sequences in my list that are not in the count. Well, there are not. I checked and re-checked and the number and the names of the sequences in the list and count are a compete match. I am using v.1.48.
I would really appreciate any and all help and thank you so much in advance.
P.S. I advocate for Mothur all the time btw.
Thanks
Noha