[Bioc-sig-seq] readAligned error

[kirti prakash]

Hi Steve,

Many thanks. I will try BAM now. The files i have been trying till now
were in .MAP form generated by bowtie.

Logically if its the ram problem then it should get solved with BAM
file. I will try to follow all the above suggestions made by you.

Thanks again,

Best regards,

Kirti Prakash

On Mon, Aug 30, 2010 at 8:48 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> On Mon, Aug 30, 2010 at 1:42 PM, kirti prakash
> <kirtiprakash3.14 at gmail.com> wrote:
>> Hi,
>>
>> I have 4gb ram and the 6 files I have vary from 500mb to 2.3gb. I am
>> trying to plot tag densities of all 6 modifications simultaneously.
>
> I guess we have successfully isolated the problem then :-)
>
>> I will follow your instructions above and see if it works and also
>> remove objects that I don't need.
>
> I guess you are only plotting certain regions of interest at a time
> (perhaps across all 6 samples at once).
>
> You might consider turning your aligned read files (what format are
> they in(?)) into BAM files, then using Rsamtools to query them.
>
> You could then, for example, query each BAM file (1 per experiment) to
> get all reads over a particular region of interest, like on Chromosome
> 1, between positions 16,000,000 and 16,500,000 (or whatever). Reading
> from BAM files like this will is *super* fast, and will save you tons
> of memory.
>
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>