[Bioc-sig-seq] readAligned error

Steve Lianoglou mailinglist.honeypot at gmail.com
Mon Aug 30 19:48:41 CEST 2010

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 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

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