[ensembl-dev] Coordinates for imported BED track data

[Sébastien Moretti]

Hi

I have just tested BED tracks with ensembl 61 and it seems that the 
coordinates problem is still there.

I can use GFF to get right coordinate mapping but BED tracks allow nice 
features like color choice for each line.

>> Hi Sébastien
>>
>> We are aware of this problem. Before we start modifying coordinates so
>> we can fix this we need to make sure that the automatic file format
>> detection always correctly identifies BED files. We are going to
>> modify the code to look at the file extension of the uploaded file as
>> well as the contents to determine format, and then for files
>> identified as BED files, adjust the coordinates internally from BED to
>> Ensembl convention. We hope to implement this for the next release.
>>
>> Steve
>
> Thanks
>
> I will wait for the next release.
>
>>> Hi,
>>>
>>> I don't know if BED tracks are officially supported in Ensembl.
>>> It seems to be the case because such data can be imported.
>>>
>>> Nevertheless, coordinates from BED tracks seem to be misinterpreted:
>>> For BED tracks, the first base in a chromosome is numbered 0.
>>> For GFF, the first base in a chromosome is numbered 1.
>>> http://genome.ucsc.edu/FAQ/FAQformat#format1
>>> http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED
>>>
>>>
>>> It means that this SNP, in GFF
>>> chr20 SNP synonymous_variation 35464269 35464269 ...
>>>
>>> must have these coordinates in BED
>>> chr20 35464268 35464269 synonymous ...
>>>
>>>
>>> In the image for this region, SNPs from BED tracks are drawn on 2
>>> nucleotides instead of one.
>>>
>>> It works if the BED track looks like this
>>> chr20 35464269 35464269 synonymous ...
>>> but it is no more an "official" BED format.
>>> (even if this fake BED syntax should continue to be interpreted for
>>> single position at least)
>>>
>>>
>>> How to solve this ?
>>>
>>> Thanks

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://bioinfo.unil.ch/