[BioC] GenomicRanges::summarizeOverlaps without strands?

[Sang Chul Choi]

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
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