You're right; it is a binary PLINK .bed file. It would be helpful to bundle
the bim bed and fam files together as a pbed item. I think the bed file is
too large to upload from the file system so I tried to upload it within a
directory of files. When I try to upload these files as a directory of
files and select "pbed" as the file format, they are not bundled together
but uploaded separately and then the bed file upload fails.
On Fri, Jul 13, 2012 at 4:31 PM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
> Hi Rob,
> The 'bed' datatype in Galaxy refers to UCSC's Browser Extensible Data
> format (http://genome.ucsc.edu/FAQ/FAQformat.html#format1).
> Is this a binary PLINK .bed file (
> http://pngu.mgh.harvard.edu/~purcell/plink/binary.shtml)? If so, you may
> want to consider looking at/using the 'pbed' datatype in Galaxy (for
> Rgenetics tools; datatype is galaxy_root/lib/galaxy/datatypes/genetics.py).
> It is a composite datatype that holds the .bim, .bed, and .fam files all
> together as a single Galaxy item. If you have a use for keeping the .bed
> file separate from the other two files, or if this is a different .bed
> file, then this doesn't apply.
> Thanks for using Galaxy,
> On Jul 12, 2012, at 5:24 PM, Robert Chase wrote:
> Hi Nate,
> I don't think that it does. We get the bed files from our GWAS pipelines.
> We were able to upload the file by adding 'bed' to the list of
> unsniffable_binary_formats in binary.py and manually specifying the format.
> Do you think this could cause problems later?
> On Thu, Jul 12, 2012 at 4:21 PM, Nate Coraor <n...@bx.psu.edu> wrote:
>> On Jul 5, 2012, at 4:15 PM, Robert Chase wrote:
>> > Hello,
>> > We tried to upload a directory of files to our local data library and
>> all uploads were successful except for one. The .bed file did not upload
>> and gave an error message; The uploaded binary file contains inappropriate
>> content. We would like to be able to share our data set with other
>> researchers using galaxy but we need to be able to upload this bed file.
>> Hi Rob,
>> Is there any chance that the file contains Unicode?
>> > -Rob
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