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INSTALLATION
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./configure
sh install-pcre.sh
./configure
make


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NOTES
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FIRE SCRIPTS:

	- fire.pl		
	- fire_maxdeg.pl 	use for restricting degeneracy of the motifs
	- fire_mbins.pl  	use for mbins
	- fire_mbins_maxdeg.pl 	use for both mbins and maxdegeneracy

NEW PARAMETERS

	For crossvalidation mode:
		--crossval=X; for X-fold crossvalidation; X is integer;	
		  for crossval can also change --corrTH=0.5 --testZth=5

	For motif degeneracy:
		--maxdegeneracy=X; where X is the maximum average degeneracy
		  of the motif per base (an N has degeneracy score 4 and A/G/C/T
		  has score 1). X is between 1 (fully defined) and 4 (most degenerate).

	For maximum frequence:
		--maxfreq=X; were X is a number btwn 0 and 1. 

	Add flanking N's for optimization:
		--add=X; where X is an integer >=0. Default is 1.

	mbins:
		--mbins=X; where is an integer X>=2
	

SEQUENCE FILES

	HUMAN:
	- hg38_r_u_X_Y.fa: where X is the number of bases upstream 
	  and Y is the number of bases downstream.
	- hg38_r_3pUTR_X.fa: where X is the length of the 3'UTR
	  padded with N's is shorter than the length
	- masked_hg38_mm10_r: sequences conserved btwn mouse and human
	- masked_multiz7way_masked_r: sequences conserved btwn 7 
	  species (human, chimp, ape, mouse, rat, dog, opossum)

		




