Loading launch_universc.sh +23 −0 Original line number Diff line number Diff line Loading @@ -160,6 +160,7 @@ Mandatory arguments to long options are mandatory for short options too. SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq SeqWell (12bp barcode, 8bp UMI): seqwell Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq SPLiT-Seq (10bp UMI, 18bp barcode): splitseq SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_" e.g. Custom (16bp barcode, 10bp UMI): custom_16_10 Loading Loading @@ -518,6 +519,8 @@ elif [[ "$technology" == "seqwell" ]] || [[ "$technology" == "seq-well" ]]; then technology="seqwell" elif [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smart-seq" ]] || [[ "$technology" == "smartseq2" ]] || [[ "$technology" == "smart-seq2" ]] || [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smart-seq2-umi" ]] || [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "smart-seq3" ]]; then technology="smartseq" elif [[ "$technology" == "splitseq" ]] || [[ "$technology" == "split-seq" ]]; then technology="splitseq" elif [[ "$technology" == "surecell" ]] || [[ "$technology" == "surecellseq" ]] || [[ "$technology" == "surecell-seq" ]] || [[ "$technology" == "ddseq" ]] || [[ "$technology" == "dd-seq" ]] || [[ "$technology" == "bioraad" ]]; then technology="surecell" elif [[ "$technology" == "custom"* ]]; then Loading Loading @@ -619,6 +622,10 @@ elif [[ "$technology" == "smartseq" ]]; then barcodelength=11 umilength=8 minlength=11 elif [[ "$technology" == "splitseq" ]]; then barcodelength=18 umilength=10 minlength=18 elif [[ "$technology" == "surecell" ]]; then barcodelength=18 umilength=8 Loading Loading @@ -1495,6 +1502,22 @@ else done fi # SPLiT-Seq can be set up similarly if a whitelist and 18bp barcode can be supported ## https://github.com/hms-dbmi/dropEst/issues/80 if [[ "$technology" == "surecell" ]]; then for convFile in "${convFiles[@]}"; do #remove phase blocks and linkers (swap UMI and barcode) sed -E ' /^([ATCGA]{92})/ { s/^(.{10})(.{8}).{30}(.{8}).{30}(.{8})*/\2\3\4\1/g n n s/^(.{10})(.{8}).{30}(.{8}).{30}(.{8})*/\2\3\4\1/g }' $convFile > ${crIN}/.temp mv ${crIN}/.temp $convFile done fi #remove adapter from SCRB-Seq if [[ "$technology" == "scrbseq" ]]; then for convFile in "${convFiles[@]}"; do Loading man/convert.sh +1 −0 Original line number Diff line number Diff line Loading @@ -110,6 +110,7 @@ Provides a conversion script to run multiple technologies and custom libraries w SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq SeqWell (12bp barcode, 8bp UMI): seqwell Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq SPLiT-Seq (10bp UMI, 18bp barcode): splitseq SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_" e.g. Custom (16bp barcode, 10bp UMI): custom_16_10 Loading Loading
launch_universc.sh +23 −0 Original line number Diff line number Diff line Loading @@ -160,6 +160,7 @@ Mandatory arguments to long options are mandatory for short options too. SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq SeqWell (12bp barcode, 8bp UMI): seqwell Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq SPLiT-Seq (10bp UMI, 18bp barcode): splitseq SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_" e.g. Custom (16bp barcode, 10bp UMI): custom_16_10 Loading Loading @@ -518,6 +519,8 @@ elif [[ "$technology" == "seqwell" ]] || [[ "$technology" == "seq-well" ]]; then technology="seqwell" elif [[ "$technology" == "smartseq" ]] || [[ "$technology" == "smart-seq" ]] || [[ "$technology" == "smartseq2" ]] || [[ "$technology" == "smart-seq2" ]] || [[ "$technology" == "smartseq2-umi" ]] || [[ "$technology" == "smart-seq2-umi" ]] || [[ "$technology" == "smartseq3" ]] || [[ "$technology" == "smart-seq3" ]]; then technology="smartseq" elif [[ "$technology" == "splitseq" ]] || [[ "$technology" == "split-seq" ]]; then technology="splitseq" elif [[ "$technology" == "surecell" ]] || [[ "$technology" == "surecellseq" ]] || [[ "$technology" == "surecell-seq" ]] || [[ "$technology" == "ddseq" ]] || [[ "$technology" == "dd-seq" ]] || [[ "$technology" == "bioraad" ]]; then technology="surecell" elif [[ "$technology" == "custom"* ]]; then Loading Loading @@ -619,6 +622,10 @@ elif [[ "$technology" == "smartseq" ]]; then barcodelength=11 umilength=8 minlength=11 elif [[ "$technology" == "splitseq" ]]; then barcodelength=18 umilength=10 minlength=18 elif [[ "$technology" == "surecell" ]]; then barcodelength=18 umilength=8 Loading Loading @@ -1495,6 +1502,22 @@ else done fi # SPLiT-Seq can be set up similarly if a whitelist and 18bp barcode can be supported ## https://github.com/hms-dbmi/dropEst/issues/80 if [[ "$technology" == "surecell" ]]; then for convFile in "${convFiles[@]}"; do #remove phase blocks and linkers (swap UMI and barcode) sed -E ' /^([ATCGA]{92})/ { s/^(.{10})(.{8}).{30}(.{8}).{30}(.{8})*/\2\3\4\1/g n n s/^(.{10})(.{8}).{30}(.{8}).{30}(.{8})*/\2\3\4\1/g }' $convFile > ${crIN}/.temp mv ${crIN}/.temp $convFile done fi #remove adapter from SCRB-Seq if [[ "$technology" == "scrbseq" ]]; then for convFile in "${convFiles[@]}"; do Loading
man/convert.sh +1 −0 Original line number Diff line number Diff line Loading @@ -110,6 +110,7 @@ Provides a conversion script to run multiple technologies and custom libraries w SCRB-Seq (6bp barcode, 10bp UMI): scrbseq, mcscrbseq SeqWell (12bp barcode, 8bp UMI): seqwell Smart-seq2-UMI, Smart-seq3 (11bp barcode, 8bp UMI): smartseq SPLiT-Seq (10bp UMI, 18bp barcode): splitseq SureCell (18bp barcode, 8bp UMI): surecell, ddseq, biorad Custom inputs are also supported by giving the name "custom" and length of barcode and UMI separated by "_" e.g. Custom (16bp barcode, 10bp UMI): custom_16_10 Loading
