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

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