Hi, Yes, you can use summarizeOverlaps() without strand information. You can reset the strand to "*" for the 'query' or just set ignore.strand = TRUE when calling summarizeOverlaps(). For details of how to set the strand see ?strand. If your bam file does not have strand information readBamGappedAlignments() should read the data into a GappedAlignments class with strand "*". Valerie On 04/05/2012 02:24 PM, Sang Chul Choi wrote: > I might answer to my question. Maybe I could just set "+" to all of the features not "*". I think strand(GappedAlignments object)<- '+' would set '+' to all of the reads. But, I will appreciate if someone answer whether this approach would do what I want. > > Thank you, > > SangChul > > On Apr 5, 2012, at 5:03 PM, Sang Chul Choi wrote: > >> Hi, >> >> Can I use GenomicRanges::summarizeOverlaps without strand information? I have short reads without strand information, and I want to count them on GRanges object. Can I simply set strand "*" for both GRanges object and GappedAlignments object? If that is the case, can I use readBamGappedAlignments to set strand "*"? >> >> Thank you, >> >> SangChul >> _______________________________________________ >> 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 > _______________________________________________ > 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