[ensembl-dev] list of chromosomes in an organism

[Glenn Proctor]

MT in this case is the mitochondrial DNA.

Glenn.


On Fri, Nov 12, 2010 at 3:41 PM, Anne Parker <ap5 at sanger.ac.uk> wrote:
> There is no Y chromosome in the cow genome, because the reference genome is
> female :)
>
> On 12 Nov 2010, at 14:52, Andrea Edwards wrote:
>
>> Hi
>>
>> I made a mistake in my last message, wasn't concentrating. I should have
>> said:
>>
>> I have got a list of the chromosomes
>> in the cow genome using the perl API and the 'Y' chromosome is named MT.
>> However I can't retrieve this chromosome using either of the following
>>
>> $slice = $slice_adaptor->fetch_by_region('chromosome','Y');
>> $slice = $slice_adaptor->fetch_by_region('chromosome','MT');
>>
>> The $slice is undefined
>>
>> I did this workaround to get chromsomes 1-29, X and MT
>>
>> @slices = @{ $slice_adaptor->fetch_all('chromosome') };
>> foreach $slice (@slices) {
>>
>>   unless ($slice->seq_region_name() =~ /Un/) {
>>       .....
>>   }
>> }
>>
>> But i was curious why I couldn't get MT directly
>>
>> thanks
>>
>>
>> On 12/11/2010 14:36, Andrea Edwards wrote:
>>>
>>> hi
>>>
>>> how do you get the list of chromosomes in an organism via the perl api?
>>>
>>> I ask because I'm trying to get the cow Z chromosome and can't access it.
>>> It is labelled MT in the genome browser so I have tried
>>>
>>> $slice = $slice_adaptor->fetch_by_region('chromosome','Z');
>>> $slice = $slice_adaptor->fetch_by_region('chromosome','MT');
>>>
>>> and neither work
>>>
>>> Thanks a lot
>>>
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>>
>>
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> Anne Parker
> Ensembl Web Production Manager
> http://www.ensembl.org
>
>
>
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