Samarjeet,
 
I will not use ChIP-seq work flow for DNA-seq, Samtools can be of help.
 
 

From: Sean Davis <sdavis2@mail.nih.gov>
To: Samarjeet <p.samar.j@gmail.com>
Cc: bioconductor@r-project.org
Sent: Tuesday, October 18, 2011 9:12 AM
Subject: Re: [BioC] DNase Seq Analysis using R

Hi, Sam.

You can get a long way by treating these data as chip-seq data (though
this isn't quite the correct model most of the time), at least for a
high-level view of things.  Here is a listing of available options:

http://bioconductor.org/packages/2.8/BiocViews.html#___ChIPseq

Sean


On Tue, Oct 18, 2011 at 11:50 AM, Samarjeet <p.samar.j@gmail.com> wrote:
> Hi ,
>   Can anyone tell me if there are packages available for Dnase Seq analysis
> on R. I have two samples in the bam format (along with their index files)
> and I would like to do downstream analysis such as finding the significance
> of the association of sites to the adjoining genes and so on.
>  Thanks in advance.
>
> Sam
>
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