Loading launch_universc.sh +3 −2 Original line number Original line Diff line number Diff line Loading @@ -650,7 +650,7 @@ if [[ "$technology" == "icell8" ]]; then fi fi if [[ "$technology" == "smartseq" ]]; then if [[ "$technology" == "smartseq" ]]; then echo "***WARNING: ${technology} should only be used for kits that have UMIs***" echo "***WARNING: ${technology} should only be used for kits that have UMIs***" echo "... UMI reads will be filtered using a tag sequence which will be removed"" echo "... UMI reads will be filtered using a tag sequence which will be removed" echo "... barcodes will derived from dual indexes" echo "... barcodes will derived from dual indexes" fi fi if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrop-v3" ]]; then if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrop-v3" ]]; then Loading Loading @@ -1526,7 +1526,7 @@ else perl ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v2 ${whitelistdir} perl ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v2 ${whitelistdir} elif [[ "$technology" == "indrop-v3" ]]; then elif [[ "$technology" == "indrop-v3" ]]; then #allow for barcodes in index (I1) and R1 #allow for barcodes in index (I1) and R1 ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v3 ${whitelistdir} perl ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v3 ${whitelistdir} fi fi else else #generating permutations of ATCG of barcode length (non-standard evaluation required to run in script) #generating permutations of ATCG of barcode length (non-standard evaluation required to run in script) Loading Loading @@ -2174,6 +2174,7 @@ else sed -E '2~2s/^(.{8})(.{8}).{4}(.{6})/\1\2\3/g' > ${crIN}/.temp sed -E '2~2s/^(.{8})(.{8}).{4}(.{6})/\1\2\3/g' > ${crIN}/.temp mv ${crIN}/.temp $convFile mv ${crIN}/.temp $convFile done done fi # inDrops: migrate dual indexes to barcode # inDrops: migrate dual indexes to barcode # https://github.com/BUStools/bustools/issues/4 # https://github.com/BUStools/bustools/issues/4 if [[ "$technology" == "indrop-v3" ]]; then if [[ "$technology" == "indrop-v3" ]]; then Loading Loading
launch_universc.sh +3 −2 Original line number Original line Diff line number Diff line Loading @@ -650,7 +650,7 @@ if [[ "$technology" == "icell8" ]]; then fi fi if [[ "$technology" == "smartseq" ]]; then if [[ "$technology" == "smartseq" ]]; then echo "***WARNING: ${technology} should only be used for kits that have UMIs***" echo "***WARNING: ${technology} should only be used for kits that have UMIs***" echo "... UMI reads will be filtered using a tag sequence which will be removed"" echo "... UMI reads will be filtered using a tag sequence which will be removed" echo "... barcodes will derived from dual indexes" echo "... barcodes will derived from dual indexes" fi fi if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrop-v3" ]]; then if [[ "$technology" == "smartseq" ]] || [[ "$technology" == "indrop-v1" ]] || [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrop-v3" ]]; then Loading Loading @@ -1526,7 +1526,7 @@ else perl ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v2 ${whitelistdir} perl ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v2 ${whitelistdir} elif [[ "$technology" == "indrop-v3" ]]; then elif [[ "$technology" == "indrop-v3" ]]; then #allow for barcodes in index (I1) and R1 #allow for barcodes in index (I1) and R1 ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v3 ${whitelistdir} perl ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v3 ${whitelistdir} fi fi else else #generating permutations of ATCG of barcode length (non-standard evaluation required to run in script) #generating permutations of ATCG of barcode length (non-standard evaluation required to run in script) Loading Loading @@ -2174,6 +2174,7 @@ else sed -E '2~2s/^(.{8})(.{8}).{4}(.{6})/\1\2\3/g' > ${crIN}/.temp sed -E '2~2s/^(.{8})(.{8}).{4}(.{6})/\1\2\3/g' > ${crIN}/.temp mv ${crIN}/.temp $convFile mv ${crIN}/.temp $convFile done done fi # inDrops: migrate dual indexes to barcode # inDrops: migrate dual indexes to barcode # https://github.com/BUStools/bustools/issues/4 # https://github.com/BUStools/bustools/issues/4 if [[ "$technology" == "indrop-v3" ]]; then if [[ "$technology" == "indrop-v3" ]]; then Loading
