Loading launch_universc.sh +39 −11 Original line number Diff line number Diff line Loading @@ -74,6 +74,8 @@ Mandatory arguments to long options are mandatory for short options too. 10x Genomics (16bp barcode, 10bp UMI): 10x, chromium (v2 or v3 automatically detected) Drop-Seq (12pb barcode, 8pm UMI): nadia, dropseq iCell8 version 3 (11bp barcode, 14bp UMI): icell8 or custom CEL-Seq (6bp barcode, 6bp UMI): celseq SCRUB-Seq (6bp barcode, 10bp UMI): scrubseq Quartz-Seq2 (14bp barcodes, 8bp UMI): quartzseq2-384 Quartz-Seq2 (15bp barcodes, 8bp UMI): quartzseq2-1536 Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_" Loading Loading @@ -441,6 +443,19 @@ if [[ "$technology" == "dropseq" ]] || [[ "$technology" == "drop-seq" ]]; then echo "Running with Nadia parameters (Drop-Seq)" technology="nadia" fi if [[ "$technology" == "celseq" ]] || [[ "$technology" == "cel-seq" ]]; then echo "Running with CEL-Seq parameters (version 1)" technology="celseq" fi if [[ "$technology" == "celseq2" ]] || [[ "$technology" == "cel-seq2" ]]; then echo "Running with CEL-Seq2 parameters" technology="celseq2" fi if [[ "$technology" == "scrubseq" ]] || [[ "$technology" == "scrub-seq" ]]; then echo "Running with SCRUB-Seq parameters" technology="scrubseq" fi if [[ "$technology" == "quartz-seq2-384" ]] || [[ "$technology" == "quartzseq2-384" ]] || [[ "$technology" == "quartz-seq2-v3.1" ]] || [[ "$technology" == "quartzseq2-v3.1" ]] || [[ "$technology" == "quartzseq2v3.1" ]]; then echo "Running with Quartz-Seq2 v3.1 parameters 384 wells (14bp barcode)" technology="quartz-seq2-384" Loading Loading @@ -701,6 +716,13 @@ else barcodefile=${SDIR}/Quartz-Seq2-384_barcode.txt elif [[ "$technology" == "quartz-seq2-1536" ]]; then barcodefile=${SDIR}/Quartz-Seq2-1536_barcode.txt elif [[ "$technology" == "custom"* ]] || [[ "$technology" == "celseq" ]] || [[ "$technology" == "scrubseq" ]]; then if [[ "$technology" == "celseq" ]]; then customname="celseq" minlength=6 elif [[ "$technology" == "scrubseq" ]]; then customname="scrubseq" minlength=6 elif [[ "$technology" == "custom"* ]]; then custom=`echo $technology | grep -o "_" | wc -l` custom=$(($custom+1)) Loading @@ -711,8 +733,8 @@ else echo "Barcode length ($barcodelength) of 16 or more:" echo " ...using barcode whitelist of 16bp" fi minlength=$(( $barcodelength < 16 ? $barcodelength : 16 )) fi # compute custom barcodes if barcode length is different barcodefile=${SDIR}/${customname}_${minlength}_barcode.txt if [[ ! -f ${barcodefile} ]]; then Loading Loading @@ -814,6 +836,12 @@ elif [[ "$technology" == "nadia" ]]; then elif [[ "$technology" == "icell8" ]]; then barcodelength=11 umilength=14 elif [[ "$technology" == "celseq" ]]; then barcodelength=6 umilength=6 elif [[ "$technology" == "scrubseq" ]]; then barcodelength=6 umilength=10 elif [[ "$technology" == "quartz-seq2-384" ]]; then barcodelength=14 umilength=8 Loading Loading
launch_universc.sh +39 −11 Original line number Diff line number Diff line Loading @@ -74,6 +74,8 @@ Mandatory arguments to long options are mandatory for short options too. 10x Genomics (16bp barcode, 10bp UMI): 10x, chromium (v2 or v3 automatically detected) Drop-Seq (12pb barcode, 8pm UMI): nadia, dropseq iCell8 version 3 (11bp barcode, 14bp UMI): icell8 or custom CEL-Seq (6bp barcode, 6bp UMI): celseq SCRUB-Seq (6bp barcode, 10bp UMI): scrubseq Quartz-Seq2 (14bp barcodes, 8bp UMI): quartzseq2-384 Quartz-Seq2 (15bp barcodes, 8bp UMI): quartzseq2-1536 Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_" Loading Loading @@ -441,6 +443,19 @@ if [[ "$technology" == "dropseq" ]] || [[ "$technology" == "drop-seq" ]]; then echo "Running with Nadia parameters (Drop-Seq)" technology="nadia" fi if [[ "$technology" == "celseq" ]] || [[ "$technology" == "cel-seq" ]]; then echo "Running with CEL-Seq parameters (version 1)" technology="celseq" fi if [[ "$technology" == "celseq2" ]] || [[ "$technology" == "cel-seq2" ]]; then echo "Running with CEL-Seq2 parameters" technology="celseq2" fi if [[ "$technology" == "scrubseq" ]] || [[ "$technology" == "scrub-seq" ]]; then echo "Running with SCRUB-Seq parameters" technology="scrubseq" fi if [[ "$technology" == "quartz-seq2-384" ]] || [[ "$technology" == "quartzseq2-384" ]] || [[ "$technology" == "quartz-seq2-v3.1" ]] || [[ "$technology" == "quartzseq2-v3.1" ]] || [[ "$technology" == "quartzseq2v3.1" ]]; then echo "Running with Quartz-Seq2 v3.1 parameters 384 wells (14bp barcode)" technology="quartz-seq2-384" Loading Loading @@ -701,6 +716,13 @@ else barcodefile=${SDIR}/Quartz-Seq2-384_barcode.txt elif [[ "$technology" == "quartz-seq2-1536" ]]; then barcodefile=${SDIR}/Quartz-Seq2-1536_barcode.txt elif [[ "$technology" == "custom"* ]] || [[ "$technology" == "celseq" ]] || [[ "$technology" == "scrubseq" ]]; then if [[ "$technology" == "celseq" ]]; then customname="celseq" minlength=6 elif [[ "$technology" == "scrubseq" ]]; then customname="scrubseq" minlength=6 elif [[ "$technology" == "custom"* ]]; then custom=`echo $technology | grep -o "_" | wc -l` custom=$(($custom+1)) Loading @@ -711,8 +733,8 @@ else echo "Barcode length ($barcodelength) of 16 or more:" echo " ...using barcode whitelist of 16bp" fi minlength=$(( $barcodelength < 16 ? $barcodelength : 16 )) fi # compute custom barcodes if barcode length is different barcodefile=${SDIR}/${customname}_${minlength}_barcode.txt if [[ ! -f ${barcodefile} ]]; then Loading Loading @@ -814,6 +836,12 @@ elif [[ "$technology" == "nadia" ]]; then elif [[ "$technology" == "icell8" ]]; then barcodelength=11 umilength=14 elif [[ "$technology" == "celseq" ]]; then barcodelength=6 umilength=6 elif [[ "$technology" == "scrubseq" ]]; then barcodelength=6 umilength=10 elif [[ "$technology" == "quartz-seq2-384" ]]; then barcodelength=14 umilength=8 Loading
