Hi list, I've identified what I think is a problem in my girafe analysis: I am getting ZERO overlaps between my aligned read intervals (from BAM file) and my annotation intervals from the interval_overlap function used in the girafe package. I'm pretty sure that the BAM file is ok, it inputs fine and is recognized as an "AlignedGenomeIntervals" object using class(my_bamfile). Although I'm using a subset of my dataset for troubleshooting, I've checked (with my own eyes) and there are definitely intervals in this list that do overlap with intervals from my gff file. So I suspect there is some formatting issue with my gff file, but I'm not sure what it is. I'll keep searching, but if anyone has an idea as to what could be causing this discrepancy, it would be super. karl Grad Student - UC Berkeley

On 03/31/2011 03:50 PM, karlerhard at berkeley.edu wrote: > Hi list, > > I've identified what I think is a problem in my girafe analysis: I am > getting ZERO overlaps between my aligned read intervals (from BAM file) > and my annotation intervals from the interval_overlap function used in the > girafe package. > > I'm pretty sure that the BAM file is ok, it inputs fine and is recognized > as an "AlignedGenomeIntervals" object using class(my_bamfile). Although > I'm using a subset of my dataset for troubleshooting, I've checked (with > my own eyes) and there are definitely intervals in this list that do > overlap with intervals from my gff file. > > So I suspect there is some formatting issue with my gff file, but I'm not > sure what it is. > > I'll keep searching, but if anyone has an idea as to what could be causing > this discrepancy, it would be super. You might want to provide a small, self contained, reproducible example to make it easier for others to look at this problem. Thanks! H. > > karl > > Grad Student - UC Berkeley > > _______________________________________________ > 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319