[BioC] BSgenome packages for new UCSC rn5 and galGal4 assemblies

[Hervé Pagès]

OK, thanks for the useful feedback. I was under the impression that
maybe people didn't care/need those old assemblies anymore but it
seems that it might be useful to keep them around for now. So please
forget my proposal to deprecate them in the next release.

Cheers,
H.


On 06/21/2012 06:09 PM, Kasper Daniel Hansen wrote:
> In my opinion that pretty much settles it:  I see no reason to
> deprecate these genome builds.
>
> It may be different for genomes that are still in early draft stages,
> where the improvement in the new build is sometimes so big that no-one
> in their right mind would continue to work on the old.
>
> Kasper
>
> On Thu, Jun 21, 2012 at 8:53 PM, Tim Triche, Jr.<tim.triche at gmail.com>  wrote:
>> there are plenty of experiments in GEO and elsewhere that were aligned to
>> mm8, although I don't know if you so much need the BSgenome package to deal
>> with them (i.e. as opposed to liftOver).    As recently as last year people
>> were still aligning to it
>>
>>
>> On Thu, Jun 21, 2012 at 5:43 PM, Kasper Daniel Hansen
>> <kasperdanielhansen at gmail.com>  wrote:
>>>
>>> I would prefer sacCer1 to be kept around; we have packaged data that
>>> was mapped to this version.  And it is small.
>>>
>>> I would suggest keeping mm8 around as well, but I am not working in
>>> mouse myself.  I don't know what the situation is in mouse, but plenty
>>> of people are still using hg18.  Perhaps it is the same for mouse.
>>>
>>> Kasper
>>>
>>> On Thu, Jun 21, 2012 at 4:37 PM, Hervé Pagès<hpages at fhcrc.org>  wrote:
>>>> Hi there,
>>>>
>>>> Just packaged BSgenome.Rnorvegicus.UCSC.rn5 (Rat) and
>>>> BSgenome.Ggallus.UCSC.galGal4 (Chicken), and dropped them
>>>> into our BioC 2.11 (devel) repository. They should become
>>>> available via biocLite() within the next hour or so. Note
>>>> that only the source tarballs will be available for the moment
>>>> so Windows and Mac users will need to install with:
>>>>
>>>>   install.packages(..., type="source")
>>>>
>>>> BTW, if nobody still needs them, I'd like to stop supporting mm8
>>>> (from Feb. 2006) and sacCer1 (Oct. 2003) at some point. They've
>>>> both been superseded by newer assemblies: by mm9 and sacCer2 for
>>>> a while, and more recently by mm10 and sacCer3. The current plan
>>>> is that they will be part of the next release (Bioc 2.11, October
>>>> 2012) but will be removed from Bioc 2.12 (if nobody says anything
>>>> in the meantime).
>>>>
>>>> Thanks,
>>>> H.
>>>>
>>>> --
>>>> Hervé Pagès
>>>>
>>>> Program in Computational Biology
>>>> Division of Public Health Sciences
>>>> Fred Hutchinson Cancer Research Center
>>>> 1100 Fairview Ave. N, M1-B514
>>>> P.O. Box 19024
>>>> Seattle, WA 98109-1024
>>>>
>>>> E-mail: hpages at fhcrc.org
>>>> Phone:  (206) 667-5791
>>>> Fax:    (206) 667-1319
>>>>
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>>>
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>>
>>
>>
>>
>> --
>> A model is a lie that helps you see the truth.
>>
>> Howard Skipper
>>


-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319