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
