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...{{dropped:2}}
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
