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 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 <[email protected]> wrote: > On Mon, Aug 30, 2010 at 1:25 PM, kirti prakash > <[email protected]> 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 > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
