[BioC] BSgenome package for a. thaliana

[Hervé Pagès]

Hi Oleg,

On 12/06/2010 07:25 PM, oleg at stat.berkeley.edu wrote:
> Hi, all
> I want to use genome package corresponding to TAIR9 version of a.thaliana
> genome. It seems that BSgenome makes 2 genome versions available:
> "BSgenome.Athaliana.TAIR.01222004" and "BSgenome.Athaliana.TAIR.04232008".
> After checking them out, they actually seem to be the same and represent
> an earlier version of the genome (TAIR8?).

They are not the same:

 > alphabetFrequency(BSgenome.Athaliana.TAIR.01222004::Athaliana$chr1)
       A       C       G       T       M       R       W       S       Y 
       K
9711178 5436538 5422303 9698578      76      37     124      31      85 
      53
       V       H       D       B       N       -       +
       0       0       0       0  163560       0       0
 > alphabetFrequency(BSgenome.Athaliana.TAIR.04232008::Athaliana$chr1)
       A       C       G       T       M       R       W       S       Y 
       K
9709677 5435365 5421130 9697107      76      36     124      30      82 
      53
       V       H       D       B       N       -       +
       0       0       0       0  168883       0       0


> I could probably try to put
> together TAIR9 genome using BSgenome manual, but I thought there might be
> a package out there already, since TAIR9 has been around for a while now
> (TAIR10 has been released last month). If someone knows of one, please let
> me know!

We'll take car of making those 2. As you pointed out, the ones we have
are pretty old now and we really need to provide something more recent.
I'll post back here when BSgenomes for TAIR9 and TAIR10 are available.

Cheers,
H.

>
> Oleg.
>
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-- 
Hervé Pagès

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