BSgenome.Mmusculus.UCSC.mm10 and upstream sequences.
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Diego Diez ▴ 760
@diego-diez-4520
Last seen 3.4 years ago
Japan
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)
Mus musculus BSgenome BSgenome Mus musculus BSgenome BSgenome • 1.8k views
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@herve-pages-1542
Last seen 1 day ago
Seattle, WA, United States
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) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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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) >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages at fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319
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