count ChIP-seq, RNA-seq counts at features

Jun 1, 2013 1 min read

Originally published on my old Blogger blog on June 1, 2013. Read the original post and its comments.

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

count reads at features NGS

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