Loading launch_universc.sh +24 −2 Original line number Diff line number Diff line Loading @@ -1657,7 +1657,13 @@ else if [[ $verbose ]]; then echo " generating a new barcode whitelist for ${technology}" fi if [[ "$technology" == "indrop-v"* ]]; then if [[ "$technology" == "bd-rhapsody" ]]; then if [[ ! -f ${whitelistdir}/bd_rhapsody_barcode.txt ]]; then #generates all combinations of I1-I2-R1 barcodes join -j 9999 ${whitelistdir}/bd_rhapsody_cell_label_section1.txt ${whitelistdir}/bd_rhapsody_cell_label_section2.txt | sed "s/ //g" | \ join -j 9999 - ${whitelistdir}/bd_rhapsody_cell_label_section3.txt | sed "s/ //g" > ${whitelistdir}/bd_rhapsody_barcode.txt fi elif [[ "$technology" == "indrop-v"* ]]; then if [[ "$technology" == "indrop-v1" ]] || [[ $technology"" == "indrop-v2" ]]; then perl ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v2 ${whitelistdir} elif [[ "$technology" == "indrop-v3" ]]; then Loading Loading @@ -2392,6 +2398,22 @@ else done fi #BD Rhapsody: remove adapters if [[ "$technology" == "bd-rhapsody" ]]; then echo " ...remove adapter and phase blocks for ${technology}" for convFile in "${convFiles[@]}"; do #remove phase blocks and linkers sed -E ' /.*(.{9})ACTGGCCTGCGA(.{9})GGTAGCGGTGACA(.{9})(.{8})/ { s/.*(.{9})ACTGGCCTGCGA(.{9})GGTAGCGGTGACA(.{9})(.{8})/\1\2\3\4/g n n s/.*(.{6}).{12}(.{6}).{13}(.{6})(.{8})/\1\2\3\4/g }' $convFile > ${crIN}/.temp mv ${crIN}/.temp $convFile done fi #inDrops: remove adapter (see links below for details) ## https://github.com/BUStools/bustools/issues/4 ## https://teichlab.github.io/scg_lib_structs/methods_html/inDrop.html Loading Loading @@ -2634,7 +2656,7 @@ else #remove phase blocks and linkers sed -E ' /.*(.{6})TAGCCATCGCATTGC(.{6})TACCTCTGAGCTGAA(.{6})ACG(.{8})GAC/ { s/.*(.{6})TAGCCATCGCATTGC(.{6})TACCTCTGAGCTGAA(.{6})ACG(.{8})GAC.*/\1\2\3\4/g s/.*(.{6})TAGCCATCGCATTGC(.{6})TACCTCTGAGCTGAA(.{6})ACG(.{8})GAC/\1\2\3\4/g n n s/.*(.{6}).{15}(.{6}).{15}(.{6}).{3}(.{8}).{3}/\1\2\3\4/g Loading whitelists/bd_rhapsody_cell_label_section1.txt 0 → 100644 +97 −0 Original line number Diff line number Diff line GTCGCTATA CTTGTACTA CTTCACATA ACACGCCGG CGGTCCAGG AATCGAATG CCTAGTATA ATTGGCTAA AAGACATGC AAGGCGATC GTGTCCTTA GGATTAGGA ATGGATCCA ACATAAGCG AACTGTATT ACCTTGCGG CAGGTGTAG AGGAGATTA GCGATTACA ACCGGATAG CCACTTGGA AGAGAAGTT TAAGTTCGA ACGGATATT TGGCTCAGA GAATCTGTA ACCAAGGAC AGTATCTGT CACACACTA ATTAAGTGC AAGTAACCC AAATCCTGT CACATTGCA GCACTGTCA ATACTTAGG GCAATCCGA ACGCAATCA GAGTATTAG GACGGATTA CAGCTGACA CAACATATT AACTTCTCC CTATGAAAT ATTATTACC TACCGAGCA TCTCTTCAA TAAGCGTTA GCCTTACAA AGCACACAG ACAGTTCCG AGTAAAGCC CAGTTTCAC CGTTACTAA TTGTTCCAA AGAAGCACT CAGCAAGAT CAAACCGCC CTAACTCGC AATATTGGG AGAACTTCC CAAAGGCAC AAGCTCAAC TCCAGTCGA AGCCATCAC AACGAGAAG CTACAGAAC AGAGCTATG GAGGATGGA TGTACCTTA ACACACAAA TCAGGAGGA GAGGTGCTA ACCCTGACC ACAAGGATC ATCCCGGAG TATGTGGCA GCTGCCAAT ATCAGAGCT TCGAAGTGA ATAGACGAG AGCCCAATC CAGAATCGT ATCTCCACA ACGAAAGGT TAGCTTGTA ACACGAGAT AACCGCCTC ATTTAGATG CAAGCAAGC CAAAGTGTG GGCAAGCAA GAGCCAATA ATGTAATGG CCTGAGCAA GAGTACATT TGCGATCTA ATCACGTTA No newline at end of file whitelists/bd_rhapsody_cell_label_section2.txt 0 → 100644 +97 −0 Original line number Diff line number Diff line TACAGGATA CACCAGGTA TGTGAAGAA GATTCATCA CACCCAAAG CACAAAGGC GTGTGTCGA CTAGGTCCT ACAGTGGTA TCGTTAGCA AGCGACACC AAGCTACTT TGTTCTCCA ACGCGAAGC CAGAAATCG ACCAAAATG AGTGTTGTC TAGGGATAC AGGGCTGGT TCATCCTAA AATCCTGAA ATCCTAGGA ACGACCACC TTCCATTGA TAGTCTTGA ACTGTTAGA ATTCATCGT ACTTCGAGC TTGCGTACA CAGTGCCCG GACACTTAA AGGAGGCGC GCCTGTTCA GTACATCTA AATCAGTTT ACGATGAAT TGACAGACA ATTAGGCAT GGAGTCTAA TAGAACACA AAATAAATA CCGACAAGA CACCTACCC AAGAGTAGA TCATTGAGA GACCTTAGA CAAGACCTA GGAATGATA AAACGTACC ACTATCCTC CCGTATCTA ACACATGTC TTGGTATGA GTGCAGTAA AGGATTCAA AGAATGGAG CTCTCTCAA GCTAACTCA ATCAACCGA ATGAGTTAC ACTTGATGA ACTTTAACT TTGGAGGTA GCCAATGTA ATCCAACCG GATGAACTG CCATGCACA TAGTGACTA AAACTGCGC ATTACCAAG CACTCGAGA AACTCATTG CTTGCTTCA ACCTGAGTC AGGTTCGCT AAGGACTAT CGTTCGGTA AGATAGTTC CAATTGATC GCATGGCTA ACCAGGTGT AGCTGCCGT TATAGCCCT AGAGGACCA ACAATATGG CAGCACTTC CACTTATGT AGTGAAAGG AACCCTCGG AGGCAGCTA AACCAAAGT GAGTGCGAA CGCTAAGCA AATTATAAC TACTAGTCA CAACAACGG CGATGTTTA No newline at end of file whitelists/bd_rhapsody_cell_label_section3.txt 0 → 100644 +97 −0 Original line number Diff line number Diff line AAGCCTTCT ATCATTCTG CACAAGTAT ACACCTTAG GAACGACAA AGTCTGTAC AAATTACAG GGCTACAGA AATGTATCG CAAGTAGAA GATCTCTTA AACAACGCG GGTGAGTTA CAGGGAGGG TCCGTCTTA TGCATAGTA ACTTACGAT TGTATGCGA GCTCCTTGA GGCACAACA CTCAAGACA ACGCTGTTG ATATTGTAA AAGTTTACG CAGCCTGGC CTATTAGCC CAAACGTGG AAAGTCATT GTCTTGGCA GATCAGCGA ACATTCGGC AGTAATTAG TGAAGCCAA TCTACGACA CATAACGTT ATGGGACTC GATAGAGGA CTACATGCG CAACGATCT GTTAGCCTA AGTTGCATC AAGGGAACT ACTACATAT CTAAGCTTC ACGAACCAG TACTTCGGA AACATCCAT AGCCTGGTT CAAGTTTCC CAGGCATTT ACGTGGGAG TCTCACGGA GCAACATTA ATGGTCCGT CTATCATGA CAATACAAG AAAGAGGCC GTAGAAGCA GCTATGGAA ACTCCAGGG ACAAGTGCA GATGGTCCA TCCTCAATA AATAAACAA CTGTACGGA CTAGATAGA AGCTATGTG AAATGGAGG AGCCGCAAG ACAGTAAAC AACGTGTGA ACTGAATTC AAGGGTCAG TGTCTATCA TCAGATTCA CACGATCCG AACAGAAAC CATGAATGA CGTACTACG TTCAGCTCA AAGGCCGCA GGTTGGACA CGTCTAGGT AATTCGGCG CAACCTCCA CAATAGGGT ACAGGCTCC ACAACTAGT AGTTGTTCT AATTACCGG ACAAACTTT TCTCGGTTA ACTAGACCG ACTCATACG ATCGAGTCT CATAGGTCA TTAGGCATA No newline at end of file Loading
launch_universc.sh +24 −2 Original line number Diff line number Diff line Loading @@ -1657,7 +1657,13 @@ else if [[ $verbose ]]; then echo " generating a new barcode whitelist for ${technology}" fi if [[ "$technology" == "indrop-v"* ]]; then if [[ "$technology" == "bd-rhapsody" ]]; then if [[ ! -f ${whitelistdir}/bd_rhapsody_barcode.txt ]]; then #generates all combinations of I1-I2-R1 barcodes join -j 9999 ${whitelistdir}/bd_rhapsody_cell_label_section1.txt ${whitelistdir}/bd_rhapsody_cell_label_section2.txt | sed "s/ //g" | \ join -j 9999 - ${whitelistdir}/bd_rhapsody_cell_label_section3.txt | sed "s/ //g" > ${whitelistdir}/bd_rhapsody_barcode.txt fi elif [[ "$technology" == "indrop-v"* ]]; then if [[ "$technology" == "indrop-v1" ]] || [[ $technology"" == "indrop-v2" ]]; then perl ${MAKEINDROPBARCODES} ${whitelistdir}/inDrop_gel_barcode1_list.txt ${whitelistdir}/inDrop_gel_barcode2_list.txt v2 ${whitelistdir} elif [[ "$technology" == "indrop-v3" ]]; then Loading Loading @@ -2392,6 +2398,22 @@ else done fi #BD Rhapsody: remove adapters if [[ "$technology" == "bd-rhapsody" ]]; then echo " ...remove adapter and phase blocks for ${technology}" for convFile in "${convFiles[@]}"; do #remove phase blocks and linkers sed -E ' /.*(.{9})ACTGGCCTGCGA(.{9})GGTAGCGGTGACA(.{9})(.{8})/ { s/.*(.{9})ACTGGCCTGCGA(.{9})GGTAGCGGTGACA(.{9})(.{8})/\1\2\3\4/g n n s/.*(.{6}).{12}(.{6}).{13}(.{6})(.{8})/\1\2\3\4/g }' $convFile > ${crIN}/.temp mv ${crIN}/.temp $convFile done fi #inDrops: remove adapter (see links below for details) ## https://github.com/BUStools/bustools/issues/4 ## https://teichlab.github.io/scg_lib_structs/methods_html/inDrop.html Loading Loading @@ -2634,7 +2656,7 @@ else #remove phase blocks and linkers sed -E ' /.*(.{6})TAGCCATCGCATTGC(.{6})TACCTCTGAGCTGAA(.{6})ACG(.{8})GAC/ { s/.*(.{6})TAGCCATCGCATTGC(.{6})TACCTCTGAGCTGAA(.{6})ACG(.{8})GAC.*/\1\2\3\4/g s/.*(.{6})TAGCCATCGCATTGC(.{6})TACCTCTGAGCTGAA(.{6})ACG(.{8})GAC/\1\2\3\4/g n n s/.*(.{6}).{15}(.{6}).{15}(.{6}).{3}(.{8}).{3}/\1\2\3\4/g Loading
whitelists/bd_rhapsody_cell_label_section1.txt 0 → 100644 +97 −0 Original line number Diff line number Diff line GTCGCTATA CTTGTACTA CTTCACATA ACACGCCGG CGGTCCAGG AATCGAATG CCTAGTATA ATTGGCTAA AAGACATGC AAGGCGATC GTGTCCTTA GGATTAGGA ATGGATCCA ACATAAGCG AACTGTATT ACCTTGCGG CAGGTGTAG AGGAGATTA GCGATTACA ACCGGATAG CCACTTGGA AGAGAAGTT TAAGTTCGA ACGGATATT TGGCTCAGA GAATCTGTA ACCAAGGAC AGTATCTGT CACACACTA ATTAAGTGC AAGTAACCC AAATCCTGT CACATTGCA GCACTGTCA ATACTTAGG GCAATCCGA ACGCAATCA GAGTATTAG GACGGATTA CAGCTGACA CAACATATT AACTTCTCC CTATGAAAT ATTATTACC TACCGAGCA TCTCTTCAA TAAGCGTTA GCCTTACAA AGCACACAG ACAGTTCCG AGTAAAGCC CAGTTTCAC CGTTACTAA TTGTTCCAA AGAAGCACT CAGCAAGAT CAAACCGCC CTAACTCGC AATATTGGG AGAACTTCC CAAAGGCAC AAGCTCAAC TCCAGTCGA AGCCATCAC AACGAGAAG CTACAGAAC AGAGCTATG GAGGATGGA TGTACCTTA ACACACAAA TCAGGAGGA GAGGTGCTA ACCCTGACC ACAAGGATC ATCCCGGAG TATGTGGCA GCTGCCAAT ATCAGAGCT TCGAAGTGA ATAGACGAG AGCCCAATC CAGAATCGT ATCTCCACA ACGAAAGGT TAGCTTGTA ACACGAGAT AACCGCCTC ATTTAGATG CAAGCAAGC CAAAGTGTG GGCAAGCAA GAGCCAATA ATGTAATGG CCTGAGCAA GAGTACATT TGCGATCTA ATCACGTTA No newline at end of file
whitelists/bd_rhapsody_cell_label_section2.txt 0 → 100644 +97 −0 Original line number Diff line number Diff line TACAGGATA CACCAGGTA TGTGAAGAA GATTCATCA CACCCAAAG CACAAAGGC GTGTGTCGA CTAGGTCCT ACAGTGGTA TCGTTAGCA AGCGACACC AAGCTACTT TGTTCTCCA ACGCGAAGC CAGAAATCG ACCAAAATG AGTGTTGTC TAGGGATAC AGGGCTGGT TCATCCTAA AATCCTGAA ATCCTAGGA ACGACCACC TTCCATTGA TAGTCTTGA ACTGTTAGA ATTCATCGT ACTTCGAGC TTGCGTACA CAGTGCCCG GACACTTAA AGGAGGCGC GCCTGTTCA GTACATCTA AATCAGTTT ACGATGAAT TGACAGACA ATTAGGCAT GGAGTCTAA TAGAACACA AAATAAATA CCGACAAGA CACCTACCC AAGAGTAGA TCATTGAGA GACCTTAGA CAAGACCTA GGAATGATA AAACGTACC ACTATCCTC CCGTATCTA ACACATGTC TTGGTATGA GTGCAGTAA AGGATTCAA AGAATGGAG CTCTCTCAA GCTAACTCA ATCAACCGA ATGAGTTAC ACTTGATGA ACTTTAACT TTGGAGGTA GCCAATGTA ATCCAACCG GATGAACTG CCATGCACA TAGTGACTA AAACTGCGC ATTACCAAG CACTCGAGA AACTCATTG CTTGCTTCA ACCTGAGTC AGGTTCGCT AAGGACTAT CGTTCGGTA AGATAGTTC CAATTGATC GCATGGCTA ACCAGGTGT AGCTGCCGT TATAGCCCT AGAGGACCA ACAATATGG CAGCACTTC CACTTATGT AGTGAAAGG AACCCTCGG AGGCAGCTA AACCAAAGT GAGTGCGAA CGCTAAGCA AATTATAAC TACTAGTCA CAACAACGG CGATGTTTA No newline at end of file
whitelists/bd_rhapsody_cell_label_section3.txt 0 → 100644 +97 −0 Original line number Diff line number Diff line AAGCCTTCT ATCATTCTG CACAAGTAT ACACCTTAG GAACGACAA AGTCTGTAC AAATTACAG GGCTACAGA AATGTATCG CAAGTAGAA GATCTCTTA AACAACGCG GGTGAGTTA CAGGGAGGG TCCGTCTTA TGCATAGTA ACTTACGAT TGTATGCGA GCTCCTTGA GGCACAACA CTCAAGACA ACGCTGTTG ATATTGTAA AAGTTTACG CAGCCTGGC CTATTAGCC CAAACGTGG AAAGTCATT GTCTTGGCA GATCAGCGA ACATTCGGC AGTAATTAG TGAAGCCAA TCTACGACA CATAACGTT ATGGGACTC GATAGAGGA CTACATGCG CAACGATCT GTTAGCCTA AGTTGCATC AAGGGAACT ACTACATAT CTAAGCTTC ACGAACCAG TACTTCGGA AACATCCAT AGCCTGGTT CAAGTTTCC CAGGCATTT ACGTGGGAG TCTCACGGA GCAACATTA ATGGTCCGT CTATCATGA CAATACAAG AAAGAGGCC GTAGAAGCA GCTATGGAA ACTCCAGGG ACAAGTGCA GATGGTCCA TCCTCAATA AATAAACAA CTGTACGGA CTAGATAGA AGCTATGTG AAATGGAGG AGCCGCAAG ACAGTAAAC AACGTGTGA ACTGAATTC AAGGGTCAG TGTCTATCA TCAGATTCA CACGATCCG AACAGAAAC CATGAATGA CGTACTACG TTCAGCTCA AAGGCCGCA GGTTGGACA CGTCTAGGT AATTCGGCG CAACCTCCA CAATAGGGT ACAGGCTCC ACAACTAGT AGTTGTTCT AATTACCGG ACAAACTTT TCTCGGTTA ACTAGACCG ACTCATACG ATCGAGTCT CATAGGTCA TTAGGCATA No newline at end of file
