[BioC] Ggallus BS genome package

[Sean MacEachern]

Hi,

I've never used them, so I may be incorrect, but I believe they are
the corresponding 1000, 2000 or 5000 bases upstream of a particular
feature on the genome (eg a probe or a gene), these may be useful for
identifying potential regulatory regions or designing custom primers
etc..

Cheers,

Sean

On Mon, May 16, 2011 at 3:22 PM, Namyoung Jung <jnamyoung at gmail.com> wrote:
> Hi, Sean
>
> I have one more question.
> Could you explain what the multiple sequences labeled as 'upstream1000,
> upstream2000, upstream5000' in the galGla3 assembly?
> Thanks.
>
>
> 2011/5/4 Sean MacEachern <sean.maceach at gmail.com>
>>
>> Hi Namyoung,
>>
>> unfortunately the Chicken genome is not as complete as many of the
>> other mammalian genomes. There is a new release that is due to come
>> out later this year, but that most likely will still be missing many
>> of the micro chromosomes. There is hope that when single molecule
>> sequencing is reliably running that this may improve things.
>>
>> Sean
>>
>> On Tue, May 3, 2011 at 1:26 PM, Namyoung Jung <jnamyoung at gmail.com> wrote:
>> > Hi,
>> > I'm a graduate student at Hopkns and working with chicken BSgenome
>> > Has anyone noticed there are some missing chromosome like 21-28 in the
>> > package?
>> > If anyone can explian this , it'll be helpful for my project.
>> > Thanks.
>> >
>> > All the best,
>> > --
>> > Namyoung Jung
>> > PhD candidate, Department of Cellular and Molecular Medicine
>> > Johns Hopkins School of Medicine, Baltimore, MD, 21205
>> > njung1 at jhmi.edu
>> >
>> >        [[alternative HTML version deleted]]
>> >
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>
>
>
> --
> Namyoung Jung
> PhD candidate, Department of Cellular and Molecular Medicine
> Johns Hopkins School of Medicine, Baltimore, MD, 21205
> njung1 at jhmi.edu
>