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

Diego Diez diego10ruiz at gmail.com
Tue Nov 5 06:35:36 CET 2013


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?

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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