7.8 years ago by
The plink/rgenetics lped and pbed (compressed) formats are special
'composite' Galaxy datatypes because the map and pedigree/genotype
need to be kept together correctly inside Galaxy. As a result, the
tool requires that the file type be specified so all of the components
be properly uploaded and stored together.
For example, to upload pbed data from your local desktop, choose
file' from the Get Data tools.
When the upload form appears, the trick is that you *must* change the
default 'Autodetect' in the first (filetype) select box to the
rgenetics datatype - either 'pbed' as the format for compressed plink
(or 'lped' for uncompressed plink genotype data) as the very first
Type the first few letters into the first box, and select the right
the list that appears.
Once this is done, you will see that the upload tool form will change
show three separate file upload inputs - one each for the plink
xxx.bed and xxx.fam where xxx is the name you set when you ran plink
create the files, or for uncompressed linkage format two separate file
upload inputs - the plink .ped and .map files.
Now you can browse for the corresponding file for each input box from
local machine - be careful not to mix them up as the upload tool is
to tell unfortunately.
At the bottom of the form, I suggest you then change the genome build
appropriate one (eg hg18 or hg19).
Finally, I'd recommend that you change the 'metadata value for
(which will be the new dataset name) to something that will remind you
the data are - something more meaningful than the default 'rgenetics'.
Click 'execute' to upload the data and create the new dataset in your
history. Compressed (pbed) format is preferred so the upload is
Note that some tools will autoconvert between lped and pbed so there
delay the first time some tools are run on a new dataset. There are
converters (use the pencil icon) also if you need them.
I hope this helps - thanks for using Galaxy and Rgenetics - please let
know how you go and feel free to contact me if you have other
On Fri, Feb 4, 2011 at 6:20 AM, BAULANDE Sylvain 211527 Partnerchip <
Ross Lazarus MBBS MPH
Associate Professor, HMS; Director of Bioinformatics, Channing
181 Longwood Ave., Boston MA 02115, USA. Tel: +1 617 505 4850
Head, Medical Bioinformatics, BakerIDI;
PO Box 6492, St Kilda Rd Central; Melbourne, VIC 8008, Australia; Tel: