[BioC] BSgenome.Mmusculus.UCSC.mm10 and upstream sequences.

[Diego Diez]

Hi Herve,

Thank you for the clarification.
Cheers,
Diego

On Tue, Nov 5, 2013 at 4:01 PM, Hervé Pagès <hpages at fhcrc.org> wrote:
> Hi Diego,
>
>
> On 11/04/2013 09:35 PM, Diego Diez wrote:
>>
>> Dear all,
>>
>> I have noticed that BSgenome.Mmusculus.UCSC.mm10 does not contain
>> entries for upstream sequences (upstream1000, upstream2000,
>> upstream5000) like for example BSgenome.Mmusculus.UCSC.mm9 does (see
>> bellow). Is there a reason for this?
>
>
> Could be that I forgot, or that it was on purpose, I can't remember.
> The plan is to deprecate the upstream sequences in BioC 2.14 and
> to remove them in BioC 2.15. This is because now we have
> getPromoterSeq() in the GenomicFeatures package, which is more
> flexible.
>
> Cheers,
> H.
>
>>
>> Thank you,
>> Diego
>>
>>
>>> library(BSgenome.Mmusculus.UCSC.mm9)
>>> Mmusculus
>>
>> Mouse genome
>> |
>> | organism: Mus musculus (Mouse)
>> | provider: UCSC
>> | provider version: mm9
>> | release date: Jul. 2007
>> | release name: NCBI Build 37
>> |
>> | single sequences (see '?seqnames'):
>> |   chr1          chr2          chr3          chr4          chr5
>> |   chr6          chr7          chr8          chr9          chr10
>> |   chr11         chr12         chr13         chr14         chr15
>> |   chr16         chr17         chr18         chr19         chrX
>> |   chrY          chrM          chr1_random   chr3_random   chr4_random
>> |   chr5_random   chr7_random   chr8_random   chr9_random  chr13_random
>> |   chr16_random  chr17_random  chrX_random   chrY_random chrUn_random
>> |
>> | multiple sequences (see '?mseqnames'):
>> |   upstream1000  upstream2000  upstream5000
>> |
>> | (use the '$' or '[[' operator to access a given sequence)
>>
>>
>>
>> library(BSgenome.Mmusculus.UCSC.mm10)
>> Mmusculus
>> Mouse genome
>> |
>> | organism: Mus musculus (Mouse)
>> | provider: UCSC
>> | provider version: mm10
>> | release date: Dec. 2011
>> | release name: Genome Reference Consortium GRCm38
>> |
>> | sequences (see '?seqnames'):
>> |   chr1                  chr2                  chr3
>> |   chr4                  chr5                  chr6
>> |   chr7                  chr8                  chr9
>> |   chr10                 chr11                 chr12
>> |   chr13                 chr14                 chr15
>> |   chr16                 chr17                 chr18
>> |   chr19                 chrX                  chrY
>> |   chrM                  chr1_GL456210_random  chr1_GL456211_random
>> |   chr1_GL456212_random  chr1_GL456213_random  chr1_GL456221_random
>> |   chr4_GL456216_random  chr4_GL456350_random  chr4_JH584292_random
>> |   chr4_JH584293_random  chr4_JH584294_random  chr4_JH584295_random
>> |   chr5_GL456354_random  chr5_JH584296_random  chr5_JH584297_random
>> |   chr5_JH584298_random  chr5_JH584299_random  chr7_GL456219_random
>> |   chrX_GL456233_random  chrY_JH584300_random  chrY_JH584301_random
>> |   chrY_JH584302_random  chrY_JH584303_random  chrUn_GL456239
>> |   chrUn_GL456359        chrUn_GL456360        chrUn_GL456366
>> |   chrUn_GL456367        chrUn_GL456368        chrUn_GL456370
>> |   chrUn_GL456372        chrUn_GL456378        chrUn_GL456379
>> |   chrUn_GL456381        chrUn_GL456382        chrUn_GL456383
>> |   chrUn_GL456385        chrUn_GL456387        chrUn_GL456389
>> |   chrUn_GL456390        chrUn_GL456392        chrUn_GL456393
>> |   chrUn_GL456394        chrUn_GL456396        chrUn_JH584304
>> |
>> | (use the '$' or '[[' operator to access a given sequence)
>>
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>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
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>
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