On 11/24/2017 01:25 PM, Ioannis Vardaxis wrote:
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
As I said there are two implementations of bowtie in Bioconductor; if
that's your preferred aligner then why not use them, from within R?
Martin
given command and then return to the package. However I try to avoid that
if possible.
Ioannis
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