7.8 years ago by
Australia
Hi, Sylvian,
The plink/rgenetics lped and pbed (compressed) formats are special
'composite' Galaxy datatypes because the map and pedigree/genotype
files
need to be kept together correctly inside Galaxy. As a result, the
upload
tool requires that the file type be specified so all of the components
can
be properly uploaded and stored together.
For example, to upload pbed data from your local desktop, choose
'Upload
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
specific
rgenetics datatype - either 'pbed' as the format for compressed plink
data
(or 'lped' for uncompressed plink genotype data) as the very first
step.
Type the first few letters into the first box, and select the right
one from
the list that appears.
Once this is done, you will see that the upload tool form will change
to
show three separate file upload inputs - one each for the plink
xxx.bim
xxx.bed and xxx.fam where xxx is the name you set when you ran plink
to
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
your
local machine - be careful not to mix them up as the upload tool is
unable
to tell unfortunately.
At the bottom of the form, I suggest you then change the genome build
to the
appropriate one (eg hg18 or hg19).
Finally, I'd recommend that you change the 'metadata value for
basename'
(which will be the new dataset name) to something that will remind you
what
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
quicker.
Note that some tools will autoconvert between lped and pbed so there
is a
delay the first time some tools are run on a new dataset. There are
built in
converters (use the pencil icon) also if you need them.
I hope this helps - thanks for using Galaxy and Rgenetics - please let
us
know how you go and feel free to contact me if you have other
questions.
On Fri, Feb 4, 2011 at 6:20 AM, BAULANDE Sylvain 211527 Partnerchip <
--
Ross Lazarus MBBS MPH
Associate Professor, HMS; Director of Bioinformatics, Channing
Laboratory;
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:
+61
385321444
