Loading iCell8_barcodes.txt→iCell8_barcode.txt +0 −0 File moved. View file launch_universc.sh +12 −9 Original line number Diff line number Diff line Loading @@ -768,6 +768,7 @@ if [[ $setup == "true" ]]; then echo " backing up whitelist of version 2 kit ..." cp 737K-august-2016.txt 737K-august-2016.txt.backup fi echo "Warning: Valid barcodes cannot be calculated accurately for Nadia or DropSeq technology" #combine 10x and Nadia barcodes cat nadia_barcode.txt 737K-august-2016.txt.backup | sort | uniq > 737K-august-2016.txt echo " whitelist converted for Nadia compatibility with version 2 kit." Loading Loading @@ -812,21 +813,23 @@ if [[ $setup == "true" ]]; then fi #create a file with every possible barcode (permutation) if [[ -f iCELL8_barcode.txt.gz ]]; then if [[ ! -f iCELL8_barcode.txt ]]; then gunzip iCELL8_barcode.txt.gz fi rm 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 echo " generating expected barcodes for iCELL8 ..." #copy known iCell8 barcodes from convert repo to cellranger install rsync -u ${SCRIPT_DIR}/iCell8_barcode.txt iCell8_barcode.txt #convert barcode whitelist to match converted barcodes sed -i 's/^/AAAAA/g' iCell8_barcodes.txt echo " imported expected barcodes for iCELL8 ..." fi echo "Valid barcodes can be calculated accurately for iCELL8" #save original barcode file (if doesn't already exist) if [[ ! -f 737K-august-2016.txt.backup ]]; then echo " backing up whitelist of version 2 kit ..." cp 737K-august-2016.txt 737K-august-2016.txt.backup fi #combine 10x and Nadia barcodes cat iCELL8_barcode.txt 737K-august-2016.txt.backup | sort | uniq > 737K-august-2016.txt #replace 10x barcodes with icell8 cat iCELL8_barcode.txt | sort | uniq > 737K-august-2016.txt echo " whitelist converted for iCELL8 compatibility with version 2 kit." #create version 3 files if version 3 whitelist available if [[ -f 3M-february-2018.txt.gz ]]; then Loading @@ -843,9 +846,9 @@ if [[ $setup == "true" ]]; then fi #combine 10x and Nadia barcodes if [[ ! -f iCELL8_barcode.txt.gz ]]; then gzip -f iCELL8_barcode.txt rm iCELL8_barcode.txt.gz fi zcat iCELL8_barcode.txt.gz 3M-february-2018.txt.backup.gz | sort | uniq > 3M-february-2018.txt cat iCELL8_barcode.txt > 3M-february-2018.txt gzip -f 3M-february-2018.txt echo " whitelist converted for iCELL8 compatibility with version 3 kit." fi Loading Loading
launch_universc.sh +12 −9 Original line number Diff line number Diff line Loading @@ -768,6 +768,7 @@ if [[ $setup == "true" ]]; then echo " backing up whitelist of version 2 kit ..." cp 737K-august-2016.txt 737K-august-2016.txt.backup fi echo "Warning: Valid barcodes cannot be calculated accurately for Nadia or DropSeq technology" #combine 10x and Nadia barcodes cat nadia_barcode.txt 737K-august-2016.txt.backup | sort | uniq > 737K-august-2016.txt echo " whitelist converted for Nadia compatibility with version 2 kit." Loading Loading @@ -812,21 +813,23 @@ if [[ $setup == "true" ]]; then fi #create a file with every possible barcode (permutation) if [[ -f iCELL8_barcode.txt.gz ]]; then if [[ ! -f iCELL8_barcode.txt ]]; then gunzip iCELL8_barcode.txt.gz fi rm 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 echo " generating expected barcodes for iCELL8 ..." #copy known iCell8 barcodes from convert repo to cellranger install rsync -u ${SCRIPT_DIR}/iCell8_barcode.txt iCell8_barcode.txt #convert barcode whitelist to match converted barcodes sed -i 's/^/AAAAA/g' iCell8_barcodes.txt echo " imported expected barcodes for iCELL8 ..." fi echo "Valid barcodes can be calculated accurately for iCELL8" #save original barcode file (if doesn't already exist) if [[ ! -f 737K-august-2016.txt.backup ]]; then echo " backing up whitelist of version 2 kit ..." cp 737K-august-2016.txt 737K-august-2016.txt.backup fi #combine 10x and Nadia barcodes cat iCELL8_barcode.txt 737K-august-2016.txt.backup | sort | uniq > 737K-august-2016.txt #replace 10x barcodes with icell8 cat iCELL8_barcode.txt | sort | uniq > 737K-august-2016.txt echo " whitelist converted for iCELL8 compatibility with version 2 kit." #create version 3 files if version 3 whitelist available if [[ -f 3M-february-2018.txt.gz ]]; then Loading @@ -843,9 +846,9 @@ if [[ $setup == "true" ]]; then fi #combine 10x and Nadia barcodes if [[ ! -f iCELL8_barcode.txt.gz ]]; then gzip -f iCELL8_barcode.txt rm iCELL8_barcode.txt.gz fi zcat iCELL8_barcode.txt.gz 3M-february-2018.txt.backup.gz | sort | uniq > 3M-february-2018.txt cat iCELL8_barcode.txt > 3M-february-2018.txt gzip -f 3M-february-2018.txt echo " whitelist converted for iCELL8 compatibility with version 3 kit." fi Loading
