New bosTau4 genome
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@herve-pages-1542
Last seen 15 hours ago
Seattle, WA, United States
Hi Miika and BioC list, I've added bosTau4 (Cow) to our list of supported genomes. Some important changes since bosTau3: - all chromosome sequences have changed: they are about 10% longer in bosTau4, - there is now a chrM sequence, - UCSC also provides the upstream sequences for bosTau4 so I've included them in BSgenome.Btaurus.UCSC.bosTau4 - I've included the full set of masks (assembly gaps, inter-contig ambiguities, RepeatMasker and Tandem Repeats Finder). I've also made a new version of BSgenome.Btaurus.UCSC.bosTau3 (version 1.3.12) that includes the full set of masks (version 1.3.11 only had the masks of assembly gaps and inter-contig ambiguities). Those 2 new packages (BSgenome.Btaurus.UCSC.bosTau4 and BSgenome.Btaurus.UCSC.bosTau4 1.3.12) are only available in the current release (BioC 2.3) and as source packages for now (the binary versions for Windows and Mac will follow soon). As always, check what genomes are available for your platform with: > library(BSgenome) > available.genomes() or use the 'type' argument to check for a specific type of package. Cheers, H. Quoting hpages at fhcrc.org: > Hi Miika, > > You are the first person to ask for it. UCSC has it too now: > > http://genome.ucsc.edu/FAQ/FAQreleases > > which is good because it's always easier to use what they provide. > I'll make it and add it to our repository as soon as possible and > will post on the Bioconductor mailing list when it's done. > > Cheers, > H. > > Quoting "Tapio, Miika (ILRI)" <m.tapio at="" cgiar.org="">: > >> Dear Herve, >> >> What is the update plan for BSgenome to have Btau4 assembly for cattle? >> Now that NBCI has updated their data-bases to match the new assembly, I >> assume you get many inquiries about it. >> >> >> >> Kind regards, >> >> Miika >> >> >> >>
BSgenome BSgenome genomes BSgenome BSgenome genomes • 847 views
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João Fadista ▴ 500
@joao-fadista-1942
Last seen 9.6 years ago
Hi Herv?, Do you know when are these 2 packages available as binary versions for Windows? Best regards, Jo?o Fadista -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor- bounces@stat.math.ethz.ch] On Behalf Of hpages@fhcrc.org Sent: Tuesday, October 28, 2008 8:20 PM To: bioconductor at stat.math.ethz.ch Cc: Tapio, Miika (ILRI) Subject: [BioC] New bosTau4 genome Hi Miika and BioC list, I've added bosTau4 (Cow) to our list of supported genomes. Some important changes since bosTau3: - all chromosome sequences have changed: they are about 10% longer in bosTau4, - there is now a chrM sequence, - UCSC also provides the upstream sequences for bosTau4 so I've included them in BSgenome.Btaurus.UCSC.bosTau4 - I've included the full set of masks (assembly gaps, inter-contig ambiguities, RepeatMasker and Tandem Repeats Finder). I've also made a new version of BSgenome.Btaurus.UCSC.bosTau3 (version 1.3.12) that includes the full set of masks (version 1.3.11 only had the masks of assembly gaps and inter-contig ambiguities). Those 2 new packages (BSgenome.Btaurus.UCSC.bosTau4 and BSgenome.Btaurus.UCSC.bosTau4 1.3.12) are only available in the current release (BioC 2.3) and as source packages for now (the binary versions for Windows and Mac will follow soon). As always, check what genomes are available for your platform with: > library(BSgenome) > available.genomes() or use the 'type' argument to check for a specific type of package. Cheers, H. Quoting hpages at fhcrc.org: > Hi Miika, > > You are the first person to ask for it. UCSC has it too now: > > http://genome.ucsc.edu/FAQ/FAQreleases > > which is good because it's always easier to use what they provide. > I'll make it and add it to our repository as soon as possible and will > post on the Bioconductor mailing list when it's done. > > Cheers, > H. > > Quoting "Tapio, Miika (ILRI)" <m.tapio at="" cgiar.org="">: > >> Dear Herve, >> >> What is the update plan for BSgenome to have Btau4 assembly for cattle? >> Now that NBCI has updated their data-bases to match the new assembly, >> I assume you get many inquiries about it. >> >> >> >> Kind regards, >> >> Miika >> >> >> >> _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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