[Bioc-devel] Question about external algorithms to Bioconductor package

[Ioannis Vardaxis]

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.morgan at 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
>> 
>
>
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