Hi Kasper, I was monitoring the processes of the computer while scanBam was running and the process is clearly CPU limited.
That's why I brought up the point. Ivan Ivan Gregoretti, PhD National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health 5 Memorial Dr, Building 5, Room 205. Bethesda, MD 20892. USA. Phone: 1-301-496-1016 and 1-301-496-1592 Fax: 1-301-496-9878 On Wed, Jul 13, 2011 at 4:45 PM, Kasper Daniel Hansen <kasperdanielhan...@gmail.com> wrote: > On Wed, Jul 13, 2011 at 4:36 PM, Ivan Gregoretti <ivang...@gmail.com> wrote: >> Hi everybody, >> >> As I wait for my large BAM to be read in by scanBAM, I can't help but to >> wonder: >> >> Has anybody tried combining scanBam with multicore to load the >> chromosomes in parallel? >> >> That would require >> >> 1) to merge the chunks at the end and >> >> 2) the original BAM to be indexed. >> >> Does anybody have any experience to share? > > Multicore will help if your task is cpu limited (and you can chunk > it). However, your specific task is probably I/O limited, in which > case it is not clear that it would help to have more cores; in fact it > might be detrimental depending on your filesystem and hardware. > > Kasper > _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing