[Genome] Bed file Format

[Brooke Rhead]

Hello Alan,

The columns of the BED file format cannot be changed or added to and 
still work in the Genome Browser.  You should know that there are three 
additional fields available in BED format that are not yet described in 
the BED format description.  The three extra fields are for displaying 
microarray-type data, and a BED file with these extra fields constitute 
a "BED 15" file.  There is a description of BED 15 on our genomewiki, here:

http://genomewiki.cse.ucsc.edu/index.php/Microarray_track

Depending on what you are planning to do with the files, you could 
consider using GFF.  If you are looking for something that you can 
upload as a custom track, however, it might not provide the solution you 
are looking for -- the extra fields in GFF (or GTF) do not show up on 
the individual items in a custom track.

If custom tracks are indeed what you are planning to use the BED file 
for, there is an option to add extra information to the individual item 
details pages.  It is done by storing the extra information in a 
web-accessible place, and then adding the url of that location to the 
custom track browser lines.  Instructions for doing this are located here:

http://genome.ucsc.edu/goldenPath/help/customTrack.html

under the heading "Step 5. (Optional) Add details pages for individual 
track features".

I hope this answers your question.  If we can be of further assistance, 
please do not hesitate to write back to this list.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Williams, Alan wrote:
> We're interested in using the BED file format but would need to add some
> additional information on a per entry (bed line) and per file basis. It
> isn't clear from the format description whether this is possible or not.
>  
> For example, we'd like to:
>  
> - add comments (ie equivalent of "#" in gff)
> - add meta info (ie equivalent of "##" in gff)
> - add extra information regarding a given bed line, perhaps as
> additional columns of information (ie a list of probe IDs from which the
> bed entry was derived)
>  
> Is it possible to do this and still have a "valid" bed file, or should
> we consider using GFF?
>  
> Thanks,
> Alan
>  
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