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Old 04-02-2013, 08:43 AM   #20
suzumar
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Location: France

Join Date: Sep 2012
Posts: 2
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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 / main.sh

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 / CreateRayInputStructures.sh

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 CreateRayInputStructures.sh script it seems to be the case, but would you please confirm it?

Marcelino
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