Maybe gmapR? 2017-11-24 16:25 GMT-02:00 Ioannis Vardaxis <ioannis.varda...@ntnu.no>:
> Hei, > > Both kalliston and salmon er for RNA data, I have DNA data. Is there any > other solution rather than Rsubread which is extremely slow? > I am making an algorithm where one of its steps should be to map the DNA > reads to the reference genome. So I would like for the user-convenience to > do it in my algorithm. But if I cannot use anything else than Rsubread > then I might write that the user at this point has to run bowtie with the > given command and then return to the package. However I try to avoid that > if possible. > > Ioannis > -- > Ioannis Vardaxis > > Stipendiat IMF > NTNU > > > > > On 24/11/2017, 19:11, "Martin Morgan" <martin.mor...@roswellpark.org> > wrote: > > >On 11/24/2017 09:57 AM, Ioannis Vardaxis wrote: > >> Hi, > >> > >> I tried the Rsubread package you suggested and the mapping is running. > >> However it takes like forever to end. Even in parallel it needs some > >>days > >> to run while bowtie for example needs only a couple of hours in 4 cores. > >> Is there any way of speeding up Rsubread? Or else I don¹t see any reason > >> using it, and this is a big problem if I cannot use bowtie inside a > >> bioconductor package. > > > >I'm not following this thread closely but there are two Bowtie > >implementations in Bioconductor > > > >http://bioconductor.org/packages/release/bioc/html/Rbowtie.html > >http://bioconductor.org/packages/release/bioc/html/Rbowtie2.html > > > >The fast solution for many problems (mapping to known transcripts) is > >kalisto / salmon, which are not available in Bioconductor -- integrating > >either of these as _libraries_ would be a nice package. > > > >Martin > > > > > >> > >> Thanks > >> > > > > > >This email message may contain legally privileged and/or confidential > >information. If you are not the intended recipient(s), or the employee > >or agent responsible for the delivery of this message to the intended > >recipient(s), you are hereby notified that any disclosure, copying, > >distribution, or use of this email message is prohibited. If you have > >received this message in error, please notify the sender immediately by > >e-mail and delete this email message from your computer. Thank you. > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
