same here, I would like to use QuasR more often, the reason I use Rsubread
(instead of say gmapR or quasR) is simply that I know where my indexed
genomes are and how to regenerate them if need be

this is a big deal for lazy people like me ;-)



On Fri, May 17, 2013 at 7:51 AM, Paul Shannon <
paul.thurmond.shannon@gmail.com> wrote:

> Thanks, Michael.
>
> May I cast my one vote, as a new user of Quasr, for an extra measure of
> transparency?  I have lost a few days to my confusion.
>
> My reasoning -- which might be idiosyncratic, and which you may find
> unconvincing -- is that if qAlign, in some invocations (but not all) needs
> to spend a few hours creating an index, and writes it to a place which is
> not entirely obvious (lib.loc), then I as a user am mightily confused.  As
> I have been! :}
>
> I would have been much better off  if qAlign had told me:
>
>   1) you specified a genome package by name for your reference
>   2) in order to use that, qAlign needs for it to be indexed
>   3) we cannot find an indexed version of that genome in your R library or
> any lib.loc directory
>   4) please specify an alternative lib.loc, and explicit path, or…
>   5) create a new index for your genome using this command:
>         buildIndexAsPackage(genomePackageName, destinationDir)  # or some
> such method call
>   6) you can then specify that newly-built index package in subsequent
> calls to qAlign this way:
>         qAlign(samplesFile, genome="~/path/to/genome-index-package.tar.gz")
>
>  - Paul
>
> On May 17, 2013, at 6:59 AM, Michael Stadler wrote:
>
> > Hi Paul,
> >
> > Please find my answers below:
> >
> > On 17.05.2013 15:01, Paul Shannon wrote:
> >> Hi Michael,
> >>
> >> Thanks for your quick and clarifying response.
> >>
> >> Since it is not possible to use pre-built indices from the bowtie
> developers, I would be glad to have a small recipe (perhaps featured
> prominently in the vignette?) which
> >>
> >>  1) explains the need for custom-built indices
> >>  2) provides (perhaps) a standalone QuasR-specific command for creating
> one
> > It is actually much simpler than you expect: qAlign() creates the index
> > automatically if it does not yet exist. The index is then saved in a
> > default location (as a new R package if your reference is a BSgenome, or
> > else in the same directory containing the fasta reference), and will be
> > automatically re-used when qAlign is called with the same reference.
> >
> >> My somewhat fuzzy grasp of the current approach is that
> >>
> >>  1) QuasR sees the string "BSgenome.Hsapiens.UCSC.hg19" on a call to
> qAlign
> >>  2) QuasR then spends a few hours building a new package with the
> proper index
> > Yes, this is described in section 5.3 of the vignette.
> >
> >>  3) and saves this package somewhere (I could not figure out where)
> > This is described in the documentation to qAlign. I agree that it would
> > be better to have this all described more explicitly in a single place,
> > so I added a description to the qAlign documentation (available shortly
> > in the development branch).
> >
> > I hope this makes it all clear.
> >
> > Best,
> > Michael
> >
>
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-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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