Great - Thanks Lukas and Matthias for your answers. My next queston: I have created a BSgenome object for my genome of interest, and it is in my current working directory. How do I make it appear under >available.genomes() Or is there a different method for accessing this object? Thanks much, --Kelly V. From: Lukas Chavez [mailto:lukas.chavez.mailings@googlemail.com] Sent: Tuesday, December 17, 2013 10:02 AM To: Vining, Kelly Cc: bioconductor@r-project.org Subject: Re: [BioC] Question about MEDIPS extend parameter Hi Kelly, yes, the extend parameter is supposed to represent the estimated average fragment size of the sonicated DNA. Lukas On Tue, Dec 17, 2013 at 5:26 AM, Vining, Kelly <kelly.vining@oregonstate.edu<mailto:kelly.vining@oregonstate.edu>> wrote: Hello BioC group, This question was already forwarded to this list (thanks Herve Pages), but I am also posting it to confirm that it has not yet been answered. I have a question about the 'extend' vs. 'shift' parameters in the MEDIPS package. From the documentation: "All reads will be extended to a length of 300nt according to the given strand information: extend=300 As an alternative to the extend parameter, the shift parameter can be specified. Here, the reads are not extended but shifted by the specified number of nucleotides with respect to the given strand information. One of the two parameters extend or shift has to be 0." Is this extend parameter supposed to represent the IP'd fragment size? Thanks for any help, --Kelly V. _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto: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]]