correct set up for version 3 (90c68232) · Commits · github_fork / Universc

launch_universc.sh

+12 −4

Original line number	Diff line number	Diff line
		@@ -335,6 +335,10 @@ if [[ $setup == "true" ]]
		cp 737K-august-2016.txt.backup 737K-august-2016.txt
		fi
		#create a file with every possible barcode (permutation)
		if [ -f nadia_barcode.txt.gz ]
		then
		gunzip nadia_barcode.txt.gz
		fi
		if [ ! -f nadia_barcode.txt ]
		then
		echo AAAA{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G} \| sed 's/ /\n/g' > nadia_barcode.txt
		@@ -368,9 +372,9 @@ if [[ $setup == "true" ]]
		#combine 10x and Nadia barcodes
		if [ ! -f nadia_barcode.txt.gz ]
		then
		gzip -k nadia_barcode.txt
		gzip nadia_barcode.txt
		fi
		zcat nadia_barcode.txt 3M-february-2018.txt.backup > 3M-february-2018.txt
		zcat nadia_barcode.txt.gz 3M-february-2018.txt.backup.gz > 3M-february-2018.txt
		gzip -f 3M-february-2018.txt
		echo "whitelist converted for Nadia compatibility with version 3 kit"
		fi
		@@ -383,6 +387,10 @@ if [[ $setup == "true" ]]
		cp 737K-august-2016.txt.backup 737K-august-2016.txt
		fi
		#create a file with every possible barcode (permutation)
		if [ -f iCELL8_barcode.txt.gz ]
		then
		gunzip iCELL8_barcode.txt.gz
		fi
		if [ ! -f iCELL8_barcode.txt ]
		then
		echo AAAAA{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G}{A,T,C,G} \| sed 's/ /\n/g' > iCELL8_barcode.txt
		@@ -416,9 +424,9 @@ if [[ $setup == "true" ]]
		#combine 10x and Nadia barcodes
		if [ ! -f iCELL8_barcode.txt.gz ]
		then
		gzip -k iCELL8_barcode.txt
		gzip iCELL8_barcode.txt
		fi
		zcat iCELL8_barcode.txt 3M-february-2018.txt.backup > 3M-february-2018.txt
		zcat iCELL8_barcode.txt.gz 3M-february-2018.txt.backup.gz > 3M-february-2018.txt
		gzip -f 3M-february-2018.txt
		echo "whitelist converted for iCELL8 compatibility with version 3 kit"
		fi

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