Hi Martin, Steve, and Michael,
I have to do some homework reading the vignettes and working on a small
subset.
Michael, I came across QuasR in my search.  Will try that.
If I got it, Rsamtools, as well as QuasR, allows reading part of the data,
say for a chromosome, thus helping in managing memory issues.
I hope I can bother you again as I will have more questions.

Thanks a lot for your prompt help.

Sincerely,
Hari



On Tue, May 14, 2013 at 3:16 AM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:

> Hi Michael,
>
> That's the first time I saw QuasR -- looks like a very nicely done package.
>
> Good stuff!
> -steve
>
>
> On Tue, May 14, 2013 at 12:06 AM, Michael Stadler
> <michael.stadler@fmi.ch> wrote:
> > Dear Hari,
> >
> > Reading all alignments of a sample (either from a bed or a bam file)
> > into memory may not be sustainable.
> >
> > One way to get around that would be to work on streams, i.e. only
> > loading a chunk of the alignments at a time. The Rsamtools package
> > provides such functionality for bam files (see ?BamFile and "yield"
> > therein).
> >
> > Alternatively, I would like to point out the QuasR package to you
> > (apologies for the advertisement). We have avoided the memory issue by
> > traversing the bam files at the C level, and only extracting the
> > information that is required. The function qQCrepoprt() may fulfill your
> > requirement 3), and the functions qCount() and qProfile() may be what
> > you can use to do 4).
> >
> > QuasR was designed to begin the analysis with reads and also create the
> > bam files for you; you can however also start with pre-existing bam
> > files and still use a good part of its functionality (see vignette
> > section 5.1, "BAM" files).
> >
> > I hope this helps,
> > Michael
> >
> >
> >
> > Reading alignments
> >
> > On 13.05.2013 15:43, Hari Easwaran wrote:
> >> Dear Bioc gurus,
> >>
> >> I am a newbie with using R tools for ChIP-seq analyses and seek advice
> on
> >> the best way to go about a data set I have.  Following are the file
> formats
> >> I have and what I would like to do with them:
> >>
> >> 1) Using Samtools, I created BED files (about 5 Gb) from the BAM files
> (3-4
> >> Gb)
> >>
> >> 2) Want to read the BED files (or BAM files) into R.
> >>
> >> 3) Perform quality control plots (like the number of duplicated reads
> >> across the samples because the nature of ChIP-seq processing is
> different
> >> in some of the samples, and so I want to know what bias it introduces).
> >>
> >> 4) Be able to retrieve specific genomic regions for exploration and
> >> visualization of reads/peaks in the context of genomic annotations (I
> guess
> >> to have in a format so that I can play with GenomicRanges).
> >>
> >>
> >> I am doing all this in a cluster with fairly good memory capacities
> (about
> >> 18G; Or perhaps I think it is 'good' memory). I went through the mailing
> >> list and found some very useful discussion on reading BED/BAM files:
> >>
> >>
> https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2011-March/001900.html
> >>
> >>
> https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2011-September/002242.html
> >>
> >> I thought BED files will be easy to work with because it already has
> data
> >> in a format that I understand (chromosome, start, end, tags). I tried
> the
> >> 'import' function from rtracklayer, as suggested in the above link, to
> read
> >> the BED file. However, it didn't work as I run out of memory.
> >>
> >>>From the discussions, it seems an alternative is Rsamtools to read BAM
> >> files.  Before I go about with trying Rsamtools, I would be happy to get
> >> some advice on whether I am on the right track by using Rsamtools, and
> if
> >> any other packages/tools might have in-built functions to achieve what I
> >> want with the data.
> >>
> >> Thanks for your time.
> >>
> >>
> >> Sincerely
> >>
> >> Hari Easwaran
> >>
> >>       [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> > --
> > --------------------------------------------
> > Michael Stadler, PhD
> > Head of Computational Biology
> > Friedrich Miescher Institute
> > Basel (Switzerland)
> > Phone : +41 61 697 6492
> > Fax   : +41 61 697 3976
> > Mail  : michael.stadler@fmi.ch
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
> --
> Steve Lianoglou
> Computational Biologist
> Department of Bioinformatics and Computational Biology
> Genentech
>

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