several tools are:
subread
http://subread.sourceforge.net/
http://bioinf.wehi.edu.au/featureCounts/
Bedtools genomecov
http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html
HTseq:
http://www-huber.embl.de/users/anders/HTSeq/doc/count.html
Homer:
http://biowhat.ucsd.edu/homer/ngs/quantification.html
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