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


--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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