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==Paper: A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements== * Allows for normalization using multiple controls: Input and IgG * Whereas most peak callers normalize the results from peak calling, this paper proposes normalizing the data before peak calling. The algorithm uses regression modeling to normalize the data and then creating dummy reads in the "normalized" data output (this can be input to MACS directly) * When testing MAX and FOXA1 chIP data: the percentage of peaks called using normalized data as input with the expected motifs is higher. Moreover, these regions with expected motifs would be missed when data is not normalized. * For MAX, both IgG and Input were available as controls, and they've found that with normalization, IgG and Input behave similarly as controls. * Installing the software: Go to github.com search "strand specific" - the program came up as the first software download before installing with "make": sudo apt-get install libgsl0-dev in Makefile: change "opt/local" to "usr" add in : "-Wl,--no-as-needed" to get: $(CC) -Wl,--no-as-needed $(CPPFLAGS) $(DFLAGS) $(GSLFLAGS_C) $(GSLFLAGS_L) src/ftumch2.cpp $(BIN_DIR)/utils.o -o $(BIN_DIR)/ftumch2 install with make copy ftumch2 to /usr/local/bin
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