[Bioc-sig-seq] readAligned error

kirti prakash kirtiprakash3.14 at gmail.com
Mon Aug 30 19:42:04 CEST 2010


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 will follow your instructions above and see if it works and also
remove objects that I don't need.

best regards,

Kirti Prakash

On Mon, Aug 30, 2010 at 8:33 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> 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

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