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.

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@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'
>> --
>> Sent via the guest posting facility at bioconductor.org.
>>
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