[BioC] GenomicRanges::summarizeOverlaps without strands?

[Valerie Obenchain]

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
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