[Bioc-sig-seq] readAligned error

[Steve Lianoglou]

On Mon, Aug 30, 2010 at 1:25 PM, kirti prakash
<kirtiprakash3.14 at gmail.com> wrote:
> Hi Steve,
>
> First of all I would like to thank you as I was able to plot tag
> densities for a couple of histone modifications.
>
> I have 6 .map files from bowtie for 6 histone modifications. So for
> first couple of files it read fine but then it gave me this error...
>
> I already had 2 readaligned data stored in my system when I read the
> 3rd file. I removed the objects by rm(me3) and tried again but again
> it gave me the error.

Perhaps you can try a different approach, which is to read each file
(or two) by itself in order to diagnose the problem.

You can do this by either utilizing the `pattern` argument in the
readAligned function, or maybe by splitting your aligned files into
two (or three) directories and reading in each directory one at a
time.

> I also think its the problem of ram but is it possible to have all the
> objects in memory as they would be needed during plotting.

How much RAM do you have?
How large are your aligned files?
What are you trying to plot?

Often times what you want to plot is some reduced representation of
your entire data -- for instance, maybe you want to plot the
distribution of phred-scores for each read? Number of mismatches?
Number of reads per chromosome, etc.

If you can't get a machine with enough horsepower to load all of your
data via readAligned in at once, perhaps you can load your data in one
at a time, do some calculation on it that you want to use for your
plot, save the result of the calculation, dispose the entire
AlignedRead object, and move onto the next one ...


-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