On Tue, Apr 13, 2010 at 6:42 AM, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:

>
>
> 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?
>>
>
>
And that's exactly what rtracklayer does. It could make your life easier.


> yes
>
> Hans
>
>
>  Cheers,
>>
>> Margherita
>>
>>
>> 2010/4/13 Hans-Rudolf Hotz<hrh@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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>
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