Matt et. al.,

I wonder if a satisfactory resolution to the issue of "the order changes 
between the GRanges object and the countBam data.frame

http://www.mail-archive.com/bioc-sig-sequencing@r-project.org/msg01144.html

I am presented with the same issue and poised to tackle it but wondr if a 
generic solution emerged from you inquiries & efforts.

Thanks,

Malcolm Cook
Stowers Institute for Medical Research -  Bioinformatics
Kansas City, Missouri  USA
 

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