From list to fasta file

Commands in mothur
1

Hi!
Is it possible to create a fasta file from .list and .count table files?

I deleted singletons from a list file, so i have a new list and count table file, now i want to create a new fasta file, that excludes the singletons, for running new cluster split command (with higher cutoff), Does it make any sense?
Thanks a lot for the help!
Yana

2

I think you are looking for the list.seqs, get.seqs and remove.seqs commands.

http://www.mothur.org/wiki/List.seqs
http://www.mothur.org/wiki/Get.seqs
http://www.mothur.org/wiki/Remove.seqs

mothur > list.seqs(count=yourCountFile) - create accnos file with the names in your list and count file.
mothur > get.seqs(fasta=yourCompleteFastaFile, accnos=current) - select those names from your full fasta file

3

Thanks, i will try it!