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

[Hervé Pagès]

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
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