Hello, I have a list of ChIP seq- CTCF binding peaks for mouse. I was wondering what would be the best way to identify if any peaks lie within 1000 bps upstream or downstream of known exons (obtained from the ref seq table, ucsc genome browser). Is there a library in R which lets me import the exon positions directly into R? Thanks in advance, Kavitha [[alternative HTML version deleted]]

Hi, Kavitha. See the GenomicFeatures package, for example. You will probably want to get familiar with the GenomicRanges package, as well. Sean On Tue, Jan 31, 2012 at 12:57 PM, Kavitha Mukund <kmukund at="" ucsd.edu=""> wrote: > Hello, > > I have a list of ChIP seq- CTCF binding peaks for mouse. I was wondering what would be the best way to identify if any peaks lie within 1000 bps upstream or downstream of known exons (obtained from the ref seq table, ucsc genome browser). > Is there a library in R which lets me import the exon positions directly into R? > > Thanks in advance, > Kavitha > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor