Reads annotation

To find overlaps between read alignments and genomic annotations, intersectBed tool in http://code.google.com/p/bedtools/ BEDTools [12] is implemented. Only read alignments which have 100% overlap with annotations are reported by setting -f option in intersectBed to 1.
For reads which can be annotated as given genomic features, detail analyses as shown below will be performed. We also explain the way how we deal with reads with multiple mapping sites and how coordinates of genomic features can be modified.