[BioC] I need BSgenome for Eucalyptus grandis

[Hervé Pagès]

Hi Lukas, Martin,

On 08/14/2013 12:29 PM, Martin Morgan wrote:
> 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

It looks like some central functions in MEDIPS expect the name of a
BSgenome data package as part of the input. But they fail if a BSgenome
object or a DNAStringSet object is supplied. Lukas, adding support
for this type of input (and maybe also for a FASTA file or FaFile
object) should be easy and would make your package much more flexible.
Don't hesitate to ask on the Bioc-devel list if you need help with this.

Cheers,
H.


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

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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