[ensembl-dev] Coordinates for imported BED track data

[Steve Searle]

Hi Sébastien

On 2 Feb 2011, at 14:59, Sébastien Moretti wrote:

> 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.
>

Sorry this wasn't in the initial 61 release. I've just put a fix in to  
the web code to correct the handling of BED file coordinates. This is  
now live on the website.

Regards

Steve

>>> 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/
>
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