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 -- ____________________________________________________ Klaudyna Borewicz M.Sc, B.Sc Department of Veterinary and Biomedical Sciences University of Minnesota 1971 Commonwealth Ave. St. Paul, Minnesota 55108 Phone: (612)624-6226 FAX: (612)625-5203 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
