Hello,
The Galaxy instance for LEfSe is run by another group. If you haven't done so already, it might be best to contact them directly to see what their suggestions are. The contact link is on the home page, in the middle pane, last sentence: http://huttenhower.org/galaxy/
Hopefully they will be able to help you transform the data into the correct format,
Best,
Jen Galaxy team
On 10/20/11 11:26 AM, Klaudyna Borewicz wrote:
Hi, I would like to use Galaxy to run LEfSe, but I don't know how to get the data into tabular format that is required (http://huttenhower.org/galaxy/tool_runner?tool_id=LEfSe_for). My data is 454 fasta files that I was analyzing with RDP to get the classification. It works fine, I get .txt file that i can load to Galaxy, it looks like this: norank Root 37646 unclassified_Root 9 domain Bacteria 37637 unclassified_Bacteria 5998 phylum OD1 0 unclassified_OD1 0 genus OD1_genera_incertae_sedis 0 phylum BRC1 0 unclassified_BRC1 0 genus BRC1_genera_incertae_sedis 0 phylum Deferribacteres 0 unclassified_"Deferribacteres" 0 class Deferribacteres 0 unclassified_Deferribacteres 0 order Deferribacterales 0 unclassified_Deferribacterales 0 family Deferribacterales_incertae_sedis 0 unclassified_Deferribacterales_incertae_sedis 0 genus Caldithrix 0 family Deferribacteraceae 0 unclassified_Deferribacteraceae 0 genus Calditerrivibrio 0 genus Mucispirillum 0 .....
but i need to have the labels in a hierarchical organization and I cannot find the way to get it to work. Please let me know if you have any suggestions, or maybe RDP is just not the way to go.
Thank you and hope to hear from you soon, Klaudyna