[Bioc-sig-seq] coordinates 0-indexed or 1-indexed in IRanges?

[Hans-Rudolf Hotz]

On 04/13/2010 03:26 PM, margherita mutarelli wrote:
> Thank you very much,
> your example was very clear and dissipated my doubts!
>
> This also means that when creating a bed file to be visualized in the UCSC
> browser from an IRanges object, the start column should be converted again
> to 0-index, by subtracting 1 to the start of the coordinates, to visualize
> it correctly, shouldn't it?

yes

Hans

> Cheers,
>
> Margherita
>
>
> 2010/4/13 Hans-Rudolf Hotz<hrh at fmi.ch>
>
>>
>>
>> this topic always causes problems. As far as I understand the situation,
>> you have to add 1 to the start of the coordinates you have downloaded (I
>> assume a BED files) from UCSC.
>>
>> Let me try and explain with a simple example:
>>
>> [...]
>>
>>
>> play with the 'upload custom track' (using the small BED file from above)
>> tool on the UCSC genome browser in case this is stil confusing
>>
>>
>> Hans
>>
>
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>
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