[BioC] I need BSgenome for Eucalyptus grandis

[Martin Morgan]

On 08/14/2013 12:22 PM, Lukas Chavez wrote:
> Hi Rodrigo,
>
> i) expecting you have the DNA sequence of Eucalyptus grandis, you can
> generate a custom genome by following the instructions you find when
> following he link Marc just sent.

I'm not sure what purpose the BSgenome package is used for; pointing 
Rsamtools::FaFile (perhaps after Rsamtools::indexFa) to your fasta file might be 
a sufficient alternative, e.g., method?"getSeq,FaFile" to get the sequences in 
regions of interest

Martin

>
> ii) MEDIPS was not designed for the analysis of MRE-seq. Certainly, you can
> easily count the number of mapped reads at genome wide windows, but there
> are no further MRE-seq specific functions available (i.e. MEDIPS does not
> apply any additional constraints that the 5′ end of a read must map to the
> CpG site within a methyl-sensitive restriction enzyme site, and no MRE-seq
> specific scores are calculated (which are inverse to MeDIP signals as I
> understand?).
>
> All the best,
> Lukas
>
>
> On Wed, Aug 14, 2013 at 11:55 AM, Marc Carlson <mcarlson at fhcrc.org> wrote:
>
>> Hi Rodrigo,
>>
>> Maybe you should have a look at the vignette here?
>>
>> http://www.bioconductor.org/**packages/release/bioc/**
>> vignettes/BSgenome/inst/doc/**BSgenomeForge.pdf<http://www.bioconductor.org/packages/release/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf>
>>
>>
>>   Marc
>>
>>
>>
>>
>>
>>
>> On 08/13/2013 05:23 PM, Rodrigo Hasbun [guest] wrote:
>>
>>> Hi
>>>
>>> I am a young researcher initiating in the use of short sequences
>>> generated by NGS for methylation analysis. Currently I am working with
>>> MRE-seq in Eucalyptus grandis and I would like to apply MEDIPs for my
>>> analysis . The problem is that I have not a BSgenome for this species. It
>>> is possible that you generate?
>>>
>>> Best
>>>
>>> Rodrigo
>>>
>>>    -- output of sessionInfo():
>>>
>>>   forgeBSgenomeDataPkg("path/to/**my/seed")
>>>>
>>> Error: no se pudo encontrar la funci'on "forgeBSgenomeDataPkg"
>>>
>>>> library(BSgenome)
>>>>
>>> Loading required package: GenomicRanges
>>> Mensajes de aviso perdidos
>>> 1: package 'BSgenome' was built under R version 2.12.1
>>> 2: package 'GenomicRanges' was built under R version 2.12.1
>>>
>>>> forgeBSgenomeDataPkg("path/to/**my/seed")
>>>>
>>> Error en .readSeedFile(x, verbose = verbose) :
>>>     seed file 'path/to/my/seed' not found
>>>
>>>> forgeBSgenomeDataPkg(/Volumes/**Datos/SeqEuca)
>>>>
>>> Error: inesperado '/' en "forgeBSgenomeDataPkg(/"
>>>
>>>> forgeBSgenomeDataPkg(Volumes/**Datos/SeqEuca)
>>>>
>>> Error en forgeBSgenomeDataPkg(Volumes/**Datos/SeqEuca) :
>>>     error in evaluating the argument 'x' in selecting a method for
>>> function 'forgeBSgenomeDataPkg'
>>>
>>>> forgeBSgenomeDataPkg(Volumes/**Datos/SeqEuca)
>>>>
>>> Error en forgeBSgenomeDataPkg(Volumes/**Datos/SeqEuca) :
>>>     error in evaluating the argument 'x' in selecting a method for
>>> function 'forgeBSgenomeDataPkg'
>>> --
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