[Bioc-sig-seq] Loading large BAM files

[Ivan Gregoretti]

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
<kasperdanielhansen at gmail.com> wrote:
> On Wed, Jul 13, 2011 at 4:36 PM, Ivan Gregoretti <ivangreg at 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
>