Loading launch_universc.sh +33 −8 Original line number Diff line number Diff line Loading @@ -198,6 +198,9 @@ Mandatory arguments to long options are mandatory for short options too. 10x Genomics version 2 (16 bp barcode, 10 bp UMI): 10x-v2, chromium-v2 10x Genomics version 3 (16 bp barcode, 12 bp UMI): 10x-v3, chromium-v3 BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1 C1 CAGE (16 bp, No UMI): c1-cage C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq CEL-Seq (8 bp barcode, 4 bp UMI): celseq CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2 Drop-Seq (12 bp barcode, 8 bp UMI): dropseq Loading @@ -213,7 +216,7 @@ Mandatory arguments to long options are mandatory for short options too. QuartzSeq (6 bp index, no UMI): quartz-seq Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384 Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536 RamDA-Seq (6 bp index, no UMI): ramda-seq RamDA-Seq (16 bp barcode, no UMI): ramda-seq SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2 SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3 SCIFI-Seq (27 bp barcode, 8 bp UMI Loading Loading @@ -614,6 +617,10 @@ elif [[ "$technology" == "10x-v2" ]] || [[ "$technology" == "chromium-v2" ]]; th technology="10x-v2" elif [[ "$technology" == "10x-v3" ]] || [[ "$technology" == "chromium-v3" ]]; then technology="10x-v3" elif [[ "$technology" == "c1" ]] || [[ "$technology" == "c1-fluidigm" ]] || [[ "$technology" == "fluidigm" ]] || [[ "$technology" == "fluidigm-c1" ]]|| [[ "$technology" == "fluidigmc1" ]] || [[ "$technology" == "c1-rna-seq" ]]|| [[ "$technology" == "c1-mrna-seq" ]] || [[ "$technology" == "c1-rnaseq" ]]|| [[ "$technology" == "c1-scrna" ]]; then technology="fluidigm-c1" elif [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "c1cage" ]] || [[ "$technology" == "cage-c1" ]] || [[ "$technology" == "cagec1" ]]; then technology="c1-cage" elif [[ "$technology" == "celseq" ]] || [[ "$technology" == "cel-seq" ]]; then technology="celseq" elif [[ "$technology" == "celseq2" ]] || [[ "$technology" == "cel-seq2" ]]; then Loading Loading @@ -649,6 +656,9 @@ elif [[ "$technology" == "quartz-seq2-1536" ]] || [[ "$technology" == "quartzseq elif [[ "$technology" == "rambda-seq" ]] || [[ "$technology" == "lamda-seq" ]] || [[ "$technology" == "lambda-seq" ]] || [[ "$technology" == "ramdaseq" ]] || [[ "$technology" == "ram-da-seq" ]] || [[ "$technology" == "ramda-seq" ]]; then technology="ramda-seq" nonUMI=true elif [[ "$technology" == "rambda-seq-c1" ]] || [[ "$technology" == "lamda-seq-c1" ]] || [[ "$technology" == "lambda-seq-c1" ]] || [[ "$technology" == "ramdaseqc1" ]] || [[ "$technology" == "ram-da-seq-c1" ]] || [[ "$technology" == "ramda-seq-c1" ]] || [[ "$technology" == "ramda-seqc1" ]] [[ "$technology" == "c1-rambda-seq" ]] || [[ "$technology" == "c1-lamda-seq" ]] || [[ "$technology" == "c1-lambda-seq" ]] || [[ "$technology" == "c1-ramdaseq" ]] || [[ "$technology" == "c1-ram-da-seq" ]] || [[ "$technology" == "c1ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]]; then technology="c1-ramda-seq" nonUMI=true elif [[ "$technology" == "sciseq" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "sci-rna-seq" ]]; then technology="sciseq3" elif [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sci-seq2" ]]; then Loading Loading @@ -706,9 +716,9 @@ if [[ $verbose ]]; then fi if [[ "$technology" == "icell8" ]]; then echo "***WARNING: ${technology} should only be used for kits that have valid UMIs***" echo "***WARNING: ${technology}-v3 should only be used for kits that have valid UMIs***" fi if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smartseq3" ]]; then if [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smartseq3" ]]; then echo "***WARNING: ${technology} should only be used for kits that have UMIs***" echo "... UMI reads will be filtered using a tag sequence which will be removed" echo "... barcodes will derived from dual indexes" Loading Loading @@ -748,6 +758,14 @@ elif [[ "$technology" == "bd-rhapsody" ]]; then barcodelength=27 umilength=8 minlength=27 elif [[ "$technology" == "fluidigm-c1" ]]; then barcodelength=16 umilength=0 minlength=16 elif [[ "$technology" == "c1-cage" ]]; then barcodelength=16 umilength=0 minlength=16 elif [[ "$technology" == "celseq" ]]; then barcodelength=8 umilength=4 Loading Loading @@ -788,12 +806,18 @@ elif [[ "$technology" == "marsseq-v2" ]]; then barcodelength=7 umilength=8 minlength=7 elif [[ "$technology" == "quartz-seq" ]] && [[ "$technology" == "ramda-seq" ]]; then elif [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]; then barcodelength=16 if [[ $nonUMI ]]; then umilength=0 fi minlength=16 elif [[ "$technology" == "quartz-seq" ]]; then barcodelength=6 if [[ $nonUMI ]]; then umilength=0 fi minlength=6 elif [[ "$technology" == "quartz-seq2-384" ]]; then barcodelength=14 umilength=8 Loading Loading @@ -877,9 +901,10 @@ if [[ -n $chemistry ]]; then [[ "$chemistry" != "SC3Pv2" ]] && \ [[ "$chemistry" != "SC3Pv3" ]] && \ [[ "$chemistry" != "SC5P-PE" ]] && \ [[ "$chemistry" != "SC5P-R1" ]] && \ [[ "$chemistry" != "SC5P-R2" ]] && \ [[ "$chemistry" != "SC-FB" ]]; then echo "Error: option -c can be auto, threeprime, fiveprime, SC3Pv1, SC3Pv2, SC3Pv3, SC5P-PE, SC5P-R2, or SC-FB" echo "Error: option -c can be auto, threeprime, fiveprime, SC3Pv1, SC3Pv2, SC3Pv3, SC5P-PE, SC5P-R1, SC5P-R2, or SC-FB" exit 1 fi fi Loading @@ -889,7 +914,7 @@ temp_chemistry="SC3Pv2" if [[ $umilength -gt 10 ]]; then temp_chemistry="SC3Pv3" fi if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smartseq3" ]];then if [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "smartseq2" ]] || [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "strt-seq"* ]]; then temp_chemistry="SC5P-PE" fi if [[ "$technology" == "10x" ]]; then Loading Loading
launch_universc.sh +33 −8 Original line number Diff line number Diff line Loading @@ -198,6 +198,9 @@ Mandatory arguments to long options are mandatory for short options too. 10x Genomics version 2 (16 bp barcode, 10 bp UMI): 10x-v2, chromium-v2 10x Genomics version 3 (16 bp barcode, 12 bp UMI): 10x-v3, chromium-v3 BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1 C1 CAGE (16 bp, No UMI): c1-cage C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq CEL-Seq (8 bp barcode, 4 bp UMI): celseq CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2 Drop-Seq (12 bp barcode, 8 bp UMI): dropseq Loading @@ -213,7 +216,7 @@ Mandatory arguments to long options are mandatory for short options too. QuartzSeq (6 bp index, no UMI): quartz-seq Quartz-Seq2 (14 bp barcode, 8 bp UMI): quartzseq2-384 Quartz-Seq2 (15 bp barcode, 8 bp UMI): quartzseq2-1536 RamDA-Seq (6 bp index, no UMI): ramda-seq RamDA-Seq (16 bp barcode, no UMI): ramda-seq SCI-Seq 2-level indexing (30 bp barcode, 8 bp UMI): sciseq2 SCI-Seq 3-level indexing (40 bp barcode, 8 bp UMI): sciseq3 SCIFI-Seq (27 bp barcode, 8 bp UMI Loading Loading @@ -614,6 +617,10 @@ elif [[ "$technology" == "10x-v2" ]] || [[ "$technology" == "chromium-v2" ]]; th technology="10x-v2" elif [[ "$technology" == "10x-v3" ]] || [[ "$technology" == "chromium-v3" ]]; then technology="10x-v3" elif [[ "$technology" == "c1" ]] || [[ "$technology" == "c1-fluidigm" ]] || [[ "$technology" == "fluidigm" ]] || [[ "$technology" == "fluidigm-c1" ]]|| [[ "$technology" == "fluidigmc1" ]] || [[ "$technology" == "c1-rna-seq" ]]|| [[ "$technology" == "c1-mrna-seq" ]] || [[ "$technology" == "c1-rnaseq" ]]|| [[ "$technology" == "c1-scrna" ]]; then technology="fluidigm-c1" elif [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "c1cage" ]] || [[ "$technology" == "cage-c1" ]] || [[ "$technology" == "cagec1" ]]; then technology="c1-cage" elif [[ "$technology" == "celseq" ]] || [[ "$technology" == "cel-seq" ]]; then technology="celseq" elif [[ "$technology" == "celseq2" ]] || [[ "$technology" == "cel-seq2" ]]; then Loading Loading @@ -649,6 +656,9 @@ elif [[ "$technology" == "quartz-seq2-1536" ]] || [[ "$technology" == "quartzseq elif [[ "$technology" == "rambda-seq" ]] || [[ "$technology" == "lamda-seq" ]] || [[ "$technology" == "lambda-seq" ]] || [[ "$technology" == "ramdaseq" ]] || [[ "$technology" == "ram-da-seq" ]] || [[ "$technology" == "ramda-seq" ]]; then technology="ramda-seq" nonUMI=true elif [[ "$technology" == "rambda-seq-c1" ]] || [[ "$technology" == "lamda-seq-c1" ]] || [[ "$technology" == "lambda-seq-c1" ]] || [[ "$technology" == "ramdaseqc1" ]] || [[ "$technology" == "ram-da-seq-c1" ]] || [[ "$technology" == "ramda-seq-c1" ]] || [[ "$technology" == "ramda-seqc1" ]] [[ "$technology" == "c1-rambda-seq" ]] || [[ "$technology" == "c1-lamda-seq" ]] || [[ "$technology" == "c1-lambda-seq" ]] || [[ "$technology" == "c1-ramdaseq" ]] || [[ "$technology" == "c1-ram-da-seq" ]] || [[ "$technology" == "c1ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]]; then technology="c1-ramda-seq" nonUMI=true elif [[ "$technology" == "sciseq" ]] || [[ "$technology" == "sci-seq" ]] || [[ "$technology" == "sci-rna-seq" ]]; then technology="sciseq3" elif [[ "$technology" == "sciseq2" ]] || [[ "$technology" == "sci-seq2" ]]; then Loading Loading @@ -706,9 +716,9 @@ if [[ $verbose ]]; then fi if [[ "$technology" == "icell8" ]]; then echo "***WARNING: ${technology} should only be used for kits that have valid UMIs***" echo "***WARNING: ${technology}-v3 should only be used for kits that have valid UMIs***" fi if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smartseq3" ]]; then if [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smartseq3" ]]; then echo "***WARNING: ${technology} should only be used for kits that have UMIs***" echo "... UMI reads will be filtered using a tag sequence which will be removed" echo "... barcodes will derived from dual indexes" Loading Loading @@ -748,6 +758,14 @@ elif [[ "$technology" == "bd-rhapsody" ]]; then barcodelength=27 umilength=8 minlength=27 elif [[ "$technology" == "fluidigm-c1" ]]; then barcodelength=16 umilength=0 minlength=16 elif [[ "$technology" == "c1-cage" ]]; then barcodelength=16 umilength=0 minlength=16 elif [[ "$technology" == "celseq" ]]; then barcodelength=8 umilength=4 Loading Loading @@ -788,12 +806,18 @@ elif [[ "$technology" == "marsseq-v2" ]]; then barcodelength=7 umilength=8 minlength=7 elif [[ "$technology" == "quartz-seq" ]] && [[ "$technology" == "ramda-seq" ]]; then elif [[ "$technology" == "ramda-seq" ]] || [[ "$technology" == "c1-ramda-seq" ]; then barcodelength=16 if [[ $nonUMI ]]; then umilength=0 fi minlength=16 elif [[ "$technology" == "quartz-seq" ]]; then barcodelength=6 if [[ $nonUMI ]]; then umilength=0 fi minlength=6 elif [[ "$technology" == "quartz-seq2-384" ]]; then barcodelength=14 umilength=8 Loading Loading @@ -877,9 +901,10 @@ if [[ -n $chemistry ]]; then [[ "$chemistry" != "SC3Pv2" ]] && \ [[ "$chemistry" != "SC3Pv3" ]] && \ [[ "$chemistry" != "SC5P-PE" ]] && \ [[ "$chemistry" != "SC5P-R1" ]] && \ [[ "$chemistry" != "SC5P-R2" ]] && \ [[ "$chemistry" != "SC-FB" ]]; then echo "Error: option -c can be auto, threeprime, fiveprime, SC3Pv1, SC3Pv2, SC3Pv3, SC5P-PE, SC5P-R2, or SC-FB" echo "Error: option -c can be auto, threeprime, fiveprime, SC3Pv1, SC3Pv2, SC3Pv3, SC5P-PE, SC5P-R1, SC5P-R2, or SC-FB" exit 1 fi fi Loading @@ -889,7 +914,7 @@ temp_chemistry="SC3Pv2" if [[ $umilength -gt 10 ]]; then temp_chemistry="SC3Pv3" fi if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smartseq3" ]];then if [[ "$technology" == "c1-cage" ]] || [[ "$technology" == "smartseq2" ]] || [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "strt-seq"* ]]; then temp_chemistry="SC5P-PE" fi if [[ "$technology" == "10x" ]]; then Loading
