fixed bug when restriction site file sent in (12979fb0) · Commits · Chaos / chaos.juicer

AWS/scripts/juicer.sh

+0 −1

Original line number	Diff line number	Diff line
		@@ -238,7 +238,6 @@ case $site in
		*) ligation="XXXX"
		echo "$site not listed as recognized enzyme. Using $site_file as site file"
		echo "Ligation junction is undefined"
		exit 100
		esac

		## If DNAse-type experiment, no fragment maps

+0 −13

Original line number	Diff line number	Diff line
		@@ -234,26 +234,13 @@ fi
		## Set ligation junction based on restriction enzyme
		case $site in
		HindIII) ligation="AAGCTAGCTT";;
		MseI) ligation="TTATAA";;
		DpnII) ligation="GATCGATC";;
		MboI) ligation="GATCGATC";;
		NlaIII) ligation="CATG";;
		NcoI) ligation="CCATGCATGG";;
		MspI) ligation="CCGCGG";;
		HinP1I) ligation="GCGCGC";;
		StyD4I) ligation="CCNGGCCNGG";;
		SaII) ligation="GTCGATCGAC";;
		NheI) ligation="GCTAGCTAGC";;
		StyI) ligation="CCWWGCWWGG";;
		XhoI) ligation="CTCGATCGAG";;
		merge) ligation="GATCGATC";;
		BglII) ligation="AGATCGATCT";;
		CviJI) ligation="'AGCC\|GGCT\|AGCT\|GGCC\|GGGG\|GGGA\|AGGG\|CCCT\|CCCC\|TCCC\|AGAG\|CTCT'";;
		none) ligation="XXXX";;
		*) ligation="XXXX"
		echo "$site not listed as recognized enzyme. Using $site_file as site file"
		echo "Ligation junction is undefined"
		exit 100
		esac

		## If DNAse-type experiment, no fragment maps