View Single Post
Old 04-02-2013, 08:43 AM   #20
Junior Member
Location: France

Join Date: Sep 2012
Posts: 2

Hi Sebastian and thanks for developing Ray. I am working on a sponge metagenome (ion torrent) and I am trying to setup ray for taxonomy and communities.

I an trying to setup the files for the latest version of greengenes (2012_08) and have parsed the information in the fasta file to the same format as 2011_01, and I am trying to manually run the script

Paper-Replication-2012 / Build-Input-Files-for-GreenGenes-Taxonomy /

and have one question regarding fasta files for Ray Taxonomy and Communities

I have notices that for the NCBI taxonomy the script Paper-Replication-2012 / Build-Input-Files-for-NCBI-Taxonomy /

Creates a single fasta file with for each genome. My question is whether those reference fasta files are just a concatenation of all .fna files associated with anty given genome. (and so there are multiples IDs and accessions associated with a given "genome". This becomes an is an issue for draft genomes (lots of scaffolds) or eukaryotic chromosomes, which I will have to "manually merge"

Actually after I double checked the script it seems to be the case, but would you please confirm it?

suzumar is offline   Reply With Quote