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 > > � � � �[[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 > _______________________________________________ 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 [[alternative HTML version deleted]]