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,

Dan


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?
> 
> -Rob
> 
> 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?
> 
> --nate
> 
> >
> > -Rob
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