dear Galaxy users, I would like to import genotyping data in Rgenetics and I can't succeed. I have ped file and map file, I try to import them in lped format but it didn't work ... Anybody with experience can help me to solve this issue ? Many thanks in advance, Best regards, Sylvain
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 < sylvain.baulande@cea.fr> wrote:
dear Galaxy users, I would like to import genotyping data in Rgenetics and I can't succeed. I have ped file and map file, I try to import them in lped format but it didn't work ... Anybody with experience can help me to solve this issue ? Many thanks in advance, Best regards, Sylvain
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-- 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
Dear Ross, Thank you form your prompt answer. unfortunately I still get an error message which is : "An error occurred running this job: *A required composite data file was not provided (RgeneticsData.ped)" *I did exactly what you mentioned except that my ped and map files have been uploaded using the ftp procedure. Do you have any clues ? Thank you so much for your help, Sylvain * * 2011/2/3 Ross <ross.lazarus@gmail.com>
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 < sylvain.baulande@cea.fr> wrote:
dear Galaxy users, I would like to import genotyping data in Rgenetics and I can't succeed. I have ped file and map file, I try to import them in lped format but it didn't work ... Anybody with experience can help me to solve this issue ? Many thanks in advance, Best regards, Sylvain
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
-- 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
Hi Sylvain, This issue has been fixed in changeset 5207:72d560d3e7fd and will be available the next time that the main server is updated, which should be within the next few weeks. Thanks for reporting this error and please let us know if we can provide additional assistance. Thanks for using Galaxy, Dan On Feb 3, 2011, at 6:05 PM, Sylvain Baulande wrote:
Dear Ross, Thank you form your prompt answer. unfortunately I still get an error message which is : "An error occurred running this job: A required composite data file was not provided (RgeneticsData.ped)" I did exactly what you mentioned except that my ped and map files have been uploaded using the ftp procedure. Do you have any clues ? Thank you so much for your help, Sylvain
2011/2/3 Ross <ross.lazarus@gmail.com> 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 <sylvain.baulande@cea.fr> wrote: dear Galaxy users, I would like to import genotyping data in Rgenetics and I can't succeed. I have ped file and map file, I try to import them in lped format but it didn't work ... Anybody with experience can help me to solve this issue ? Many thanks in advance, Best regards, Sylvain
_______________________________________________ galaxy-user mailing list galaxy-user@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-user
-- 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
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participants (4)
-
BAULANDE Sylvain 211527 Partnerchip -
Daniel Blankenberg -
Ross -
Sylvain Baulande