Hello all, I've been using the girafe package to make counts tables for two nascent transcript libraries (overlap between aligned reads and genes), which I am comparing directly. I would like to check if there's a difference between "sense" and "antisense" tags within genic regions. I thought I could do this easily by making the following object: library1_sense <- detail(library1[strand(library1)=="+"]) and then using it in the interval_overlap with the list of annotated genes. However, the resulting object is a data frame and not an AlignedGenomeIntervals object, which interval_overlap seems to need. Is there some way around this? Maybe a way to force strandedness in the interval_overlap function? Or another way to create a subset of "+" or "-" strand reads while maintaining the AlignedGenomeIntervals format? I've been reading the manual but I can't find a way to do this. thanks for any help you can offer! Karl Erhard Graduate Student UC Berkeley

Hello, if you omit calling the detail function, the result will be an AlignedGenomeIntervals object: library1_sense <- library1[strand(library1)=="+"] while the result of the "detail" function is a data.frame. And if the object containing the genes is of class "Genome_intervals_stranded" the strand will be taken into account, if it is of class "Genome_intervals" without strand information, the strand does not matter. Hope this answers your question. Best regards, Joern On Thu, Apr 28, 2011 at 2:44 AM, <karlerhard@berkeley.edu> wrote: > > Hello all, > > I've been using the girafe package to make counts tables for two nascent > transcript libraries (overlap between aligned reads and genes), which I am > comparing directly. I would like to check if there's a difference between > "sense" and "antisense" tags within genic regions. > > I thought I could do this easily by making the following object: > > library1_sense <- detail(library1[strand(library1)=="+"]) > > and then using it in the interval_overlap with the list of annotated > genes. However, the resulting object is a data frame and not an > AlignedGenomeIntervals object, which interval_overlap seems to need. > > Is there some way around this? Maybe a way to force strandedness in the > interval_overlap function? Or another way to create a subset of "+" or > "-" strand reads while maintaining the AlignedGenomeIntervals format? > I've been reading the manual but I can't find a way to do this. > > thanks for any help you can offer! > > > Karl Erhard > Graduate Student > UC Berkeley > [[alternative HTML version deleted]]