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

[Michael Stadler]

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