Good day, > I have DNA data. Is there any other solution rather than Rsubread which is > extremely slow?
How much of it do you have? If it's a large size, such as whole genome sequencing, then it would take longer than an RNA-seq experiment regardless of the algorithm you use. I have used Rsubread in the past and I think it performs as well as the other popular alignment programs. > I am making an algorithm where one of its steps should be to map the DNA > reads to the reference genome. Although it's possible to do short read mapping with packages like Rbowtie, I don't think this preprocessing stage should happen in R which is a statistical programming language. Modularity is good. -------------------------------------- Dario Strbenac University of Sydney Camperdown NSW 2050 Australia _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
