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 <[email protected]> wrote: > On Mon, Aug 30, 2010 at 1:42 PM, kirti prakash > <[email protected]> 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 > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
