Question: Data Format
0
Klaudyna Borewicz • 10 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
--
____________________________________________________
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
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modified 7.1 years ago
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Jennifer Hillman Jackson ♦ 25k
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written
7.1 years ago by
Klaudyna Borewicz • 10
