[BioC] QuasR: how to use an indexed reference genome?

[Michael Stadler]

Dear Martin,

Thank you for pointing out AnnotationHub - it seems that this could
indeed be a way to host pre-generated alignment indices.

We have internally discussed the option of providing pre-built indices
to the community and came to the conclusion that with our current
resources, we would not be able to create and maintain the various
flavours of indices for current and future BSgenome packages. In
addition to the "standard" alignment index, there are two more indices
for bisulfite alignments per genome. Furthermore, for each additional
aligner supported by QuasR in the future, another set of indices will
have to be added.

Given that QuasR can generate and re-use those indices locally, we do
not consider this a priority.

Michael and Dimos


On 18.05.2013 02:31, Martin Morgan wrote:
> On 05/16/2013 11:41 PM, Michael Stadler wrote:
>> If more people would prefer to use pre-built indices, and if the BioC
>> agrees to host such big packages, it would also be conceivable to
>> provide index packages corresponding to the BSgenome packages for
>> download.
> 
> We've been experimenting with AnnotationHub (the package, and the cloud
> resource --
> http://bioconductor.org/packages/release/bioc/html/AnnotationHub.html)
> as a way to provide large(r) data without having to go through the full
> formalism of creating packages; perhaps the indexes are a good case for
> this? The user or software would then
> 
>   library(AnnotationHub)
>   hub = AnnotationHub()
>   hub$<tab>
>   ## the preceeding works, now for hypothetical...!
>   hub$bioconductor.QuasR.BSgenome<tab>
> 
> and when hitting <return> on a complete name the AnnotationHub would do
> the right thing, downloading and installing the index in an appropriate
> place (including, e.g., caching in the AnnotationHub cache, if that's
> appropriate...)
> 
> Martin
> 

-- 
--------------------------------------------
Michael Stadler, PhD
Head of Computational Biology
Friedrich Miescher Institute
Basel (Switzerland)
Phone : +41 61 697 6492
Fax   : +41 61 697 3976
Mail  : michael.stadler at fmi.ch