Loading test/run_tests_smartseq3_local.sh +7 −12 Original line number Diff line number Diff line Loading @@ -27,7 +27,7 @@ while [[ ! -f /home/tom/repos/universc/test-10x-hek293t/outs/metrics_summary.csv done # test manual setup bash launch_universc.sh -t "smartseq3" --setup --barcodefile "whitelists/test_bcs_small.txt" bash launch_universc.sh -t "smartseq3" --setup --barcodefile "whitelists/test_bcs_smartseq3_hek293t.txt" if [[ -d input4cellranger_test-smartseq3-hek293t-test-chr21 ]]; then rm -rf input4cellranger_test-smartseq3-hek293t-test-chr21 Loading @@ -47,14 +47,9 @@ fi bash launch_universc.sh --id "test-smartseq3-hek293t-test-chr21" --technology "smartseq3" \ --chemistry "SC5P-PE" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R1_001.fastq.gz" \ --read2 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R2_001.fastq.gz" \ --index1 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_I1_001.fastq.gz" \ --index2 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_I2_001.fastq.gz" \ --barcodefile "whitelists/Smartseq3_diySpike_small_bcs.txt" \ --per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1 if [ -f test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R1_001.fastq ]; then rename "s/_S1_L001//" test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_[IR][12]_001.fastq* rename "s/_001//" test/shared/smartseq3-test/Smartseq3_diySpike_[IR][12]_001.fastq* fi --barcodefile "whitelists/test_bcs_smartseq3_hek293t.txt" \ --read1 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R1_001.fastq" \ --read2 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R2_001.fastq" \ --index1 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_I1_001.fastq" \ --index2 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_I2_001.fastq" \ --per-cell-data --jobmode "local" --verbose #--as-is # "local" --localcores 1 test/run_tests_smartseq3_local_diyspike.sh +6 −14 Original line number Diff line number Diff line Loading @@ -22,13 +22,10 @@ if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ fi # compress all input files if [[ -f test/shared/smartseq3-test/Smartseq3.diySpike.R1.fastq ]]; then echo gzip test/shared/smartseq3-test//Smartseq3.diySpike*fastq if [[ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_S1_R1_001.fastq ]]; then echo gzip test/shared/smartseq3-test/Smartseq3_diySpike_S1_L00?_S1_[IR][12]_001.fastq.gz fi rename -f "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_[IR][12]_001.fastq rename -f "s/_001//" test/shared/smartseq3-test/Smartseq3_diySpike_[IR][12]_001.fastq #rename "s/Smartseq3.diySpike./Smartseq3_diySpike_/g" test/shared/smartseq3-test/Smartseq3.diySpike.[IR][12].fastq #rename "s/Smartseq3.diySpike./Smartseq3_diySpike_/g" test/shared/smartseq3-test/Smartseq3.diySpike.L001.[IR][12].fastq Loading @@ -38,7 +35,7 @@ while [[ ! -f /home/tom/repos/universc/test-10x-hek293t/outs/metrics_summary.csv done # test manual setup bash launch_universc.sh -t "smartseq3" --setup --barcodefile "whitelists/test_bcs_small.txt" bash launch_universc.sh -t "smartseq3" --setup --barcodefile "whitelists/test_bcs_smartseq3_full.txt" if [[ -d input4cellranger_test-smartseq3-diyspike-hg38 ]]; then rm -rf input4cellranger_test-smartseq3-diyspike-hg38 Loading @@ -55,14 +52,9 @@ fi bash launch_universc.sh --id "test-smartseq3-diyspike-hg38" --technology "smartseq3" \ --chemistry "SC5P-PE" \ --reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \ --read1 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq.gz" \ --barcodefile "whitelists/test_bcs_smartseq3_full.txt" \ --read1 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq" \ --read2 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq" \ --index1 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_I1_001.fastq" \ --index2 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_I2_001.fastq" \ --barcodefile "whitelists/Smartseq3_diySpike_small_bcs.txt" \ --per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1 if [ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq ]; then rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_[IR][12]_001.fastq* rename "s/_001//" test/shared/smartseq3-test/Smartseq3_diySpike_[IR][12]_001.fastq* fi --per-cell-data --jobmode "local" --verbose #--as-is # "local" --localcores 1 whitelists/test_bcs_smartseq3_hek293t.txt 0 → 100644 +492 −0 Original line number Diff line number Diff line AAAAGACGCAATGGAC AAACCGTTCAAGAGGT AAACCTCACAATGGAC AACAGACGCAATGGAC AACCCGTTCAAGAGGT AACCGATGCAATGGAC AAGACACGCAATGGAC AAGACGTTCAAGAGGT AAGAGAAGCAATGGAC AAGAGACACAATGGAC AAGAGACCCAATGGAC AAGAGACGAAATGGAC AAGAGACGCAAAGGAC AAGAGACGCAAGGGAC AAGAGACGCAATGAAC AAGAGACGCAATGCAC AAGAGACGCAATGGAA AAGAGACGCAATGGAC AAGAGACGCAATGGAG AAGAGACGCAATGGAT AAGAGACGCAATGGCC AAGAGACGCAATGGGC AAGAGACGCAATGGTC AAGAGACGCAATTGAC AAGAGACGCATTGGAC AAGAGACGCCATGGAC AAGAGACGCTATGGAC AAGAGACGGAATGGAC AAGAGACGTAATGGAC AAGAGCCGCAATGGAC AAGAGCCGCAATGGCC AAGCAGTTCAAGAGGT AAGCCATTCAAGAGGT AAGCCCTTCAAGAGGT AAGCCGATCAAGAGGT AAGCCGCTCAAGAGGT AAGCCGGTCAAGAGGT AAGCCGTACAAGAGGT AAGCCGTGCAAGAGGT AAGCCGTTAAAGAGGT AAGCCGTTCAAAAGGT AAGCCGTTCAACAGGT AAGCCGTTCAAGAAGT AAGCCGTTCAAGACGT AAGCCGTTCAAGAGAT AAGCCGTTCAAGAGCT AAGCCGTTCAAGAGGA AAGCCGTTCAAGAGGG AAGCCGTTCAAGAGGT AAGCCGTTCAAGAGTT AAGCCGTTCAAGATGT AAGCCGTTCAAGCGGT AAGCCGTTCAAGGGGT AAGCCGTTCAAGTGGT AAGCCGTTCAATAGGT AAGCCGTTCATGAGGT AAGCCGTTCCAGAGGT AAGCCGTTCTAGAGGT AAGCCGTTGAAGAGGT AAGCCGTTTAAGAGGT AAGCCTTTCAAGAGGT AAGCGACGCAATGGAC AAGCGGTTCAAGAGGT AAGGCGTTCAAGAGGT AAGTGACGCAATGGAC AATCCGTTCAAGAGGT ACATGTCTCAAGAGGT ACCAAGTCCAAGAGGT ACCTTGCTCAATGGAC ACGCCGTTCAAGAGGT AGACCAAGCAATGGAC AGAGAGTTCAATGGAC AGGCCGTTCAAGAGGT AGTCTCAACAATGGAC ATCAACAGCAATGGAC ATGAGACGCAATGGAC ATGCCGTTCAAGAGGT ATGGAACCCAATGGAC ATGGAACCCCATCCAA CAAACTCACAATGGAC CAACATCACAATGGAC CAACCACACAATGGAC CAACCACACAATGGCC CAACCCCACAATGGAC CAACCGCACAATGGAC CAACCTAACAATGGAC CAACCTCACAAAGGAC CAACCTCACAAGGGAC CAACCTCACAATAGAC CAACCTCACAATCGAC CAACCTCACAATGAAC CAACCTCACAATGCAC CAACCTCACAATGGAA CAACCTCACAATGGAC CAACCTCACAATGGAG CAACCTCACAATGGAT CAACCTCACAATGGCC CAACCTCACAATGGGC CAACCTCACAATGGTC CAACCTCACAATGTAC CAACCTCACAATTGAC CAACCTCACATTGGAC CAACCTCACCATGGAC CAACCTCACTATGGAC CAACCTCAGAATGGAC CAACCTCCCAATGGAC CAACCTCTCAATGGAC CAACCTTACAATGGAC CACAACAGCAATGGAC CACCCTCACAATGGAC CACCCTCACAATGGCC CACCCTCACAATGGTC CAGCCGTTCAAGAGGT CAGCCTCACAATGGAC CATCCTCACAATGGAC CATCCTCACAATGGTC CCACCTCACAATGGAC CCACCTCACAATGGCC CCCAAGTCCAAGAGGT CGACCTCACAATGGAC CGAGAGTTCAATGGAC CGCAACAGCAATGGAC CGCAACAGCAATGGCC CTAAACAGCAATGGAC CTACCTCACAATGGAC CTCAAAAGCAATGGAC CTCAACAACAATGGAC CTCAACACCAATGGAC CTCAACAGCAAAGGAC CTCAACAGCAAGGGAC CTCAACAGCAATCGAC CTCAACAGCAATGCAC CTCAACAGCAATGGAA CTCAACAGCAATGGAC CTCAACAGCAATGGAG CTCAACAGCAATGGAT CTCAACAGCAATGGCC CTCAACAGCAATGGGC CTCAACAGCAATGGTC CTCAACAGCAATGTAC CTCAACAGCAATTGAC CTCAACAGCATTGGAC CTCAACAGCCATGGAC CTCAACAGCTATGGAC CTCAACAGGAATGGAC CTCAACATCAATGGAC CTCAACCGCAATGGAC CTCAACTGCAATGGAC CTCAAGAGCAATGGAC CTCACCAGCAATGGAC CTCATCAGCAATGGAC CTCCACAGCAATGGAC CTCCACAGCAATGGCC CTCGACAGCAATGGAC CTCTACAGCAATGGAC CTCTACAGCAATGGCC CTGAACAGCAATGGAC CTGGAACCCAATGGAC CTGGAACCCCATCCAA GAAGAGTTCAATGGAC GAATGTCTCAAGAGGT GAGAGACGCAATGGAC GAGCCGTTCAAGAGGT GCAAGTCTCAAGAGGT GCAGAGTTCAATGGAC GCATATCTCAAGAGGT GCATCTCTCAAGAGGT GCATGACTCAAGAGGT GCATGGCTCAAGAGGT GCATGTATCAAGAGGT GCATGTCACAAGAGGT GCATGTCCCAAGAGGT GCATGTCGCAAGAGGT GCATGTCTCAAAAGGT GCATGTCTCAACAGGT GCATGTCTCAAGAAGT GCATGTCTCAAGACGT GCATGTCTCAAGAGCT GCATGTCTCAAGAGGA GCATGTCTCAAGAGGG GCATGTCTCAAGAGGT GCATGTCTCAAGAGTT GCATGTCTCAAGATGT GCATGTCTCAAGCGGT GCATGTCTCAAGTGGT GCATGTCTCAATAGGT GCATGTCTCAGGAGGT GCATGTCTCATGAGGT GCATGTCTCTAGAGGT GCATGTCTGAAGAGGT GCATGTCTTAAGAGGT GCATGTGTCAAGAGGT GCATTTCTCAAGAGGT GCCAAGTCCAAGAGGT GCCTGTCTCAAGAGGT GCCTTGCTCAATGGAC GCTCTCAACAATGGAC GCTTGTCTCAAGAGGT GCTTGTCTCAAGCGGT GGAAAGTTCAATGGAC GGACAGTTCAATGGAC GGACCAAGCAATGGAC GGACTCAACAATGGAC GGAGAATTCAATGGAC GGAGACTTCAATGGAC GGAGAGATCAATGGAC GGAGAGGTCAATGGAC GGAGAGGTCAATGGTC GGAGAGTACAATGGAC GGAGAGTACAATGGCC GGAGAGTGCAATGGAC GGAGAGTTAAATGGAC GGAGAGTTCAAAGGAC GGAGAGTTCAAGGGAC GGAGAGTTCAATAGAC GGAGAGTTCAATCGAC GGAGAGTTCAATGAAC GGAGAGTTCAATGCAC GGAGAGTTCAATGGAA GGAGAGTTCAATGGAC GGAGAGTTCAATGGAG GGAGAGTTCAATGGCC GGAGAGTTCAATGGGC GGAGAGTTCAATGGTC GGAGAGTTCAATGTAC GGAGAGTTCAATTGAC GGAGAGTTCATTGGAC GGAGAGTTCCATGGAC GGAGAGTTCGATGGAC GGAGAGTTCTATGGAC GGAGAGTTGAATGGAC GGAGCGTTCAATGGAC GGAGCGTTCAATGGCC GGAGGGTTCAATGGAC GGAGTGTTCAATGGAC GGATAGTTCAATGGAC GGATGTCTCAAGAGGT GGCGAGTTCAATGGAC GGGCTCAACAATGGAC GGGGAGTTCAATGGAC GGTATCAACAATGGAC GGTCACAACAATGGAC GGTCGCAACAATGGAC GGTCTAAACAATGGAC GGTCTCAAAAATGGAC GGTCTCAACAAAGGAC GGTCTCAACAATAGAC GGTCTCAACAATCGAC GGTCTCAACAATGAAC GGTCTCAACAATGGAA GGTCTCAACAATGGAC GGTCTCAACAATGGAG GGTCTCAACAATGGCC GGTCTCAACAATGGGC GGTCTCAACAATGGTC GGTCTCAACAATTGAC GGTCTCAACATTGGAC GGTCTCAACCATGGAC GGTCTCAACTATGGAC GGTCTCACCAATGGAC GGTCTCATCAATGGAC GGTCTCCACAATGGAC GGTCTCTACAATGGAC GGTGAGTTCAATGGAC GGTGAGTTCAATGGCC GGTGTCAACAATGGAC GTGGAACCCAATGGAC GTGGAACCCAATGGCC GTGGAACCCCATCCAA TAACCAAGCAATGGAC TACAAGTCCAAGAGGT TACAGATGCAATGGAC TACCAATGCAATGGAC TACCCATGCAATGGAC TACCGAAGCAATGGAC TACCGAGGCAATGGAC TACCGATACAATGGAC TACCGATCCAATGGAC TACCGATGCAAAGGAC TACCGATGCAAGGGAC TACCGATGCAATAGAC TACCGATGCAATCGAC TACCGATGCAATGAAC TACCGATGCAATGCAC TACCGATGCAATGGAC TACCGATGCAATGGAG TACCGATGCAATGGAT TACCGATGCAATGGCC TACCGATGCAATGGGC TACCGATGCAATGGTC TACCGATGCAATGTAC TACCGATGCAATTGAC TACCGATGCATTGGAC TACCGATGCCATGGAC TACCGATGCTATGGAC TACCGATGGAATGGAC TACCGCTGCAATGGAC TACCGTTGCAATGGAC TACGGATGCAATGGAC TACTGATGCAATGGAC TACTTGCTCAATGGAC TAGAGACGCAATGGAC TAGCCGTTCAAGAGGT TAGCGATGCAATGGAC TAGGAACCCAATGGAC TAGGAACCCCATCCAA TCAAAGTCCAAGAGGT TCACCAAGCAATGGAC TCATTGCTCAATGGAC TCATTGCTCAATGGCC TCCAAATCCAAGAGGT TCCAACTCCAAGAGGT TCCAAGACCAAGAGGT TCCAAGCCCAAGAGGT TCCAAGGCCAAGAGGT TCCAAGTACAAGAGGT TCCAAGTCAAAGAGGT TCCAAGTCCAAAAGGT TCCAAGTCCAACAGGT TCCAAGTCCAAGACGT TCCAAGTCCAAGAGAT TCCAAGTCCAAGAGCT TCCAAGTCCAAGAGGA TCCAAGTCCAAGAGGC TCCAAGTCCAAGAGGG TCCAAGTCCAAGAGGT TCCAAGTCCAAGAGTT TCCAAGTCCAAGATGT TCCAAGTCCAAGCGGT TCCAAGTCCAAGTGGT TCCAAGTCCAATAGGT TCCAAGTCCATGAGGT TCCAAGTCCCAGAGGT TCCAAGTCCGAGAGGT TCCAAGTCCTAGAGGT TCCAAGTCGAAGAGGT TCCAAGTGCAAGAGGT TCCAAGTTCAAGAGGT TCCAATTCCAAGAGGT TCCACGTCCAAGAGGT TCCAGGTCCAAGAGGT TCCATGCTCAATGGAC TCCATGCTCAATGGCC TCCATGTCCAAGAGGT TCCCAGTCCAAGAGGT TCCGAGTCCAAGAGGT TCCGTGCTCAATGGAC TCCTAGCTCAATGGAC TCCTAGTCCAAGAGGT TCCTTACTCAATGGAC TCCTTCCTCAATGGAC TCCTTGATCAATGGAC TCCTTGCACAATGGAC TCCTTGCCCAATGGAC TCCTTGCGCAATGGAC TCCTTGCTCAAAGGAC TCCTTGCTCAAGGGAC TCCTTGCTCAATAGAC TCCTTGCTCAATCGAC TCCTTGCTCAATGAAC TCCTTGCTCAATGCAC TCCTTGCTCAATGGAA TCCTTGCTCAATGGAC TCCTTGCTCAATGGAG TCCTTGCTCAATGGCC TCCTTGCTCAATGGGC TCCTTGCTCAATGGTC TCCTTGCTCAATGTAC TCCTTGCTCAATTGAC TCCTTGCTCATTGGAC TCCTTGCTCCATGGAC TCCTTGCTCGATGGAC TCCTTGCTCTATGGAC TCCTTGCTGAATGGAC TCCTTGCTTAATGGAC TCCTTGGTCAATGGAC TCCTTTCTCAATGGAC TCGAAGTCCAAGAGGT TCGGAACCCAATGGAC TCGGAACCCCATCCAA TCGTTGCTCAATGGAC TCTAAGTCCAAGAGGT TGAACAAGCAATGGAC TGACAAAGCAATGGAC TGACCAAACAATGGAC TGACCAACCAATGGAC TGACCAAGCAAAGGAC TGACCAAGCAAGGGAC TGACCAAGCAATAGAC TGACCAAGCAATCGAC TGACCAAGCAATGAAC TGACCAAGCAATGCAC TGACCAAGCAATGGAA TGACCAAGCAATGGAC TGACCAAGCAATGGAG TGACCAAGCAATGGAT TGACCAAGCAATGGCC TGACCAAGCAATGGGC TGACCAAGCAATGGTC TGACCAAGCAATGTAC TGACCAAGCAATTGAC TGACCAAGCATTGGAC TGACCAAGCCATGGAC TGACCAAGCTATGGAC TGACCAAGTAATGGAC TGACCAATCAATGGAC TGACCACGCAATGGAC TGACCAGGCAATGGAC TGACCATGCAATGGAC TGACCATGCAATGGCC TGACCCAGCAATGGAC TGACCTAGCAATGGAC TGACGAAGCAATGGAC TGAGAGTTCAATGGAC TGAGCAAGCAATGGAC TGCAAGTCCAAGAGGT TGCCCAAGCAATGGAC TGCCCAAGCAATGGCC TGCCCAAGCAATGGTC TGCCCAAGCATTGGAC TGCCGATGCAATGGAC TGCTTGCTCAATGGAC TGGCCAAGCAATGGAC TGGGAACCCAATGGAC TGGGAACCCCATCCAA TGTCCAAGCAATGGAC TTAGAACCCAATGGAC TTCAAGTCCAAGAGGT TTCCGATGCAATGGAC TTCGAACCCAATGGAC TTCGAACCCCATCCAA TTCTTGCTCAATGGAC TTGAAACCCAATGGAC TTGAAACCCCATCCAA TTGCAACCCAATGGAC TTGCAACCCCATCCAA TTGGAAACCAATGGAC TTGGAAACCCATCCAA TTGGAACACAATGGAC TTGGAACACCATCCAA TTGGAACCACATCCAA TTGGAACCCAAAGGAC TTGGAACCCAAGGGAC TTGGAACCCAATAGAC TTGGAACCCAATCCAA TTGGAACCCAATCGAC TTGGAACCCAATGAAC TTGGAACCCAATGCAC TTGGAACCCAATGGAA TTGGAACCCAATGGAC TTGGAACCCAATGGAG TTGGAACCCAATGGCC TTGGAACCCAATGGGC TTGGAACCCAATGGTC TTGGAACCCAATGTAC TTGGAACCCAATTGAC TTGGAACCCATTGGAC TTGGAACCCCAACCAA TTGGAACCCCATACAA TTGGAACCCCATCAAA TTGGAACCCCATCCAA TTGGAACCCCATCCAG TTGGAACCCCATCCAT TTGGAACCCCATCCCA TTGGAACCCCATCCTA TTGGAACCCCATGGAC TTGGAACCCCCTCCAA TTGGAACCCCGTCCAA TTGGAACCCCTTCCAA TTGGAACCCGATCCAA TTGGAACCCTATGGAC TTGGAACCGAATGGAC TTGGAACCGCATCCAA TTGGAACCTAATGGAC TTGGAACGCAATGGAC TTGGAAGCCAATGGAC TTGGACCCCAATGGAC TTGGACCCCAATGGCC TTGGACCCCCATCCAA TTGGAGCCCAATGGAC TTGGAGCCCCATCCAA TTGGATCCCAATGGAC TTGGATCCCCATCCAA TTGGCACCCAATGGAC TTGGCACCCAATGGCC TTGGCACCCAATGGTC TTGGCACCCCATCCAA TTGGGACCCAATGGAC TTGGGACCCCATCCAA TTGGTACCCAATGGAC TTGGTACCCCATCCAA TTTGAACCCAATGGAC Loading
test/run_tests_smartseq3_local.sh +7 −12 Original line number Diff line number Diff line Loading @@ -27,7 +27,7 @@ while [[ ! -f /home/tom/repos/universc/test-10x-hek293t/outs/metrics_summary.csv done # test manual setup bash launch_universc.sh -t "smartseq3" --setup --barcodefile "whitelists/test_bcs_small.txt" bash launch_universc.sh -t "smartseq3" --setup --barcodefile "whitelists/test_bcs_smartseq3_hek293t.txt" if [[ -d input4cellranger_test-smartseq3-hek293t-test-chr21 ]]; then rm -rf input4cellranger_test-smartseq3-hek293t-test-chr21 Loading @@ -47,14 +47,9 @@ fi bash launch_universc.sh --id "test-smartseq3-hek293t-test-chr21" --technology "smartseq3" \ --chemistry "SC5P-PE" \ --reference "test/cellranger_reference/cellranger-tiny-ref/3.0.0" \ --read1 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R1_001.fastq.gz" \ --read2 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R2_001.fastq.gz" \ --index1 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_I1_001.fastq.gz" \ --index2 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_I2_001.fastq.gz" \ --barcodefile "whitelists/Smartseq3_diySpike_small_bcs.txt" \ --per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1 if [ -f test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R1_001.fastq ]; then rename "s/_S1_L001//" test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_[IR][12]_001.fastq* rename "s/_001//" test/shared/smartseq3-test/Smartseq3_diySpike_[IR][12]_001.fastq* fi --barcodefile "whitelists/test_bcs_smartseq3_hek293t.txt" \ --read1 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R1_001.fastq" \ --read2 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R2_001.fastq" \ --index1 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_I1_001.fastq" \ --index2 "test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_I2_001.fastq" \ --per-cell-data --jobmode "local" --verbose #--as-is # "local" --localcores 1
test/run_tests_smartseq3_local_diyspike.sh +6 −14 Original line number Diff line number Diff line Loading @@ -22,13 +22,10 @@ if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ fi # compress all input files if [[ -f test/shared/smartseq3-test/Smartseq3.diySpike.R1.fastq ]]; then echo gzip test/shared/smartseq3-test//Smartseq3.diySpike*fastq if [[ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_S1_R1_001.fastq ]]; then echo gzip test/shared/smartseq3-test/Smartseq3_diySpike_S1_L00?_S1_[IR][12]_001.fastq.gz fi rename -f "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_[IR][12]_001.fastq rename -f "s/_001//" test/shared/smartseq3-test/Smartseq3_diySpike_[IR][12]_001.fastq #rename "s/Smartseq3.diySpike./Smartseq3_diySpike_/g" test/shared/smartseq3-test/Smartseq3.diySpike.[IR][12].fastq #rename "s/Smartseq3.diySpike./Smartseq3_diySpike_/g" test/shared/smartseq3-test/Smartseq3.diySpike.L001.[IR][12].fastq Loading @@ -38,7 +35,7 @@ while [[ ! -f /home/tom/repos/universc/test-10x-hek293t/outs/metrics_summary.csv done # test manual setup bash launch_universc.sh -t "smartseq3" --setup --barcodefile "whitelists/test_bcs_small.txt" bash launch_universc.sh -t "smartseq3" --setup --barcodefile "whitelists/test_bcs_smartseq3_full.txt" if [[ -d input4cellranger_test-smartseq3-diyspike-hg38 ]]; then rm -rf input4cellranger_test-smartseq3-diyspike-hg38 Loading @@ -55,14 +52,9 @@ fi bash launch_universc.sh --id "test-smartseq3-diyspike-hg38" --technology "smartseq3" \ --chemistry "SC5P-PE" \ --reference "~/reference/cellranger/refdata-cellranger-GRCh38-3.0.0" \ --read1 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq.gz" \ --barcodefile "whitelists/test_bcs_smartseq3_full.txt" \ --read1 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq" \ --read2 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R2_001.fastq" \ --index1 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_I1_001.fastq" \ --index2 "test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_I2_001.fastq" \ --barcodefile "whitelists/Smartseq3_diySpike_small_bcs.txt" \ --per-cell-data --jobmode "sge" --verbose #--as-is # "local" --localcores 1 if [ -f test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_R1_001.fastq ]; then rename "s/_S1_L001//" test/shared/smartseq3-test/Smartseq3_diySpike_S1_L001_[IR][12]_001.fastq* rename "s/_001//" test/shared/smartseq3-test/Smartseq3_diySpike_[IR][12]_001.fastq* fi --per-cell-data --jobmode "local" --verbose #--as-is # "local" --localcores 1
whitelists/test_bcs_smartseq3_hek293t.txt 0 → 100644 +492 −0 Original line number Diff line number Diff line AAAAGACGCAATGGAC AAACCGTTCAAGAGGT AAACCTCACAATGGAC AACAGACGCAATGGAC AACCCGTTCAAGAGGT AACCGATGCAATGGAC AAGACACGCAATGGAC AAGACGTTCAAGAGGT AAGAGAAGCAATGGAC AAGAGACACAATGGAC AAGAGACCCAATGGAC AAGAGACGAAATGGAC AAGAGACGCAAAGGAC AAGAGACGCAAGGGAC AAGAGACGCAATGAAC AAGAGACGCAATGCAC AAGAGACGCAATGGAA AAGAGACGCAATGGAC AAGAGACGCAATGGAG AAGAGACGCAATGGAT AAGAGACGCAATGGCC AAGAGACGCAATGGGC AAGAGACGCAATGGTC AAGAGACGCAATTGAC AAGAGACGCATTGGAC AAGAGACGCCATGGAC AAGAGACGCTATGGAC AAGAGACGGAATGGAC AAGAGACGTAATGGAC AAGAGCCGCAATGGAC AAGAGCCGCAATGGCC AAGCAGTTCAAGAGGT AAGCCATTCAAGAGGT AAGCCCTTCAAGAGGT AAGCCGATCAAGAGGT AAGCCGCTCAAGAGGT AAGCCGGTCAAGAGGT AAGCCGTACAAGAGGT AAGCCGTGCAAGAGGT AAGCCGTTAAAGAGGT AAGCCGTTCAAAAGGT AAGCCGTTCAACAGGT AAGCCGTTCAAGAAGT AAGCCGTTCAAGACGT AAGCCGTTCAAGAGAT AAGCCGTTCAAGAGCT AAGCCGTTCAAGAGGA AAGCCGTTCAAGAGGG AAGCCGTTCAAGAGGT AAGCCGTTCAAGAGTT AAGCCGTTCAAGATGT AAGCCGTTCAAGCGGT AAGCCGTTCAAGGGGT AAGCCGTTCAAGTGGT AAGCCGTTCAATAGGT AAGCCGTTCATGAGGT AAGCCGTTCCAGAGGT AAGCCGTTCTAGAGGT AAGCCGTTGAAGAGGT AAGCCGTTTAAGAGGT AAGCCTTTCAAGAGGT AAGCGACGCAATGGAC AAGCGGTTCAAGAGGT AAGGCGTTCAAGAGGT AAGTGACGCAATGGAC AATCCGTTCAAGAGGT ACATGTCTCAAGAGGT ACCAAGTCCAAGAGGT ACCTTGCTCAATGGAC ACGCCGTTCAAGAGGT AGACCAAGCAATGGAC AGAGAGTTCAATGGAC AGGCCGTTCAAGAGGT AGTCTCAACAATGGAC ATCAACAGCAATGGAC ATGAGACGCAATGGAC ATGCCGTTCAAGAGGT ATGGAACCCAATGGAC ATGGAACCCCATCCAA CAAACTCACAATGGAC CAACATCACAATGGAC CAACCACACAATGGAC CAACCACACAATGGCC CAACCCCACAATGGAC CAACCGCACAATGGAC CAACCTAACAATGGAC CAACCTCACAAAGGAC CAACCTCACAAGGGAC CAACCTCACAATAGAC CAACCTCACAATCGAC CAACCTCACAATGAAC CAACCTCACAATGCAC CAACCTCACAATGGAA CAACCTCACAATGGAC CAACCTCACAATGGAG CAACCTCACAATGGAT CAACCTCACAATGGCC CAACCTCACAATGGGC CAACCTCACAATGGTC CAACCTCACAATGTAC CAACCTCACAATTGAC CAACCTCACATTGGAC CAACCTCACCATGGAC CAACCTCACTATGGAC CAACCTCAGAATGGAC CAACCTCCCAATGGAC CAACCTCTCAATGGAC CAACCTTACAATGGAC CACAACAGCAATGGAC CACCCTCACAATGGAC CACCCTCACAATGGCC CACCCTCACAATGGTC CAGCCGTTCAAGAGGT CAGCCTCACAATGGAC CATCCTCACAATGGAC CATCCTCACAATGGTC CCACCTCACAATGGAC CCACCTCACAATGGCC CCCAAGTCCAAGAGGT CGACCTCACAATGGAC CGAGAGTTCAATGGAC CGCAACAGCAATGGAC CGCAACAGCAATGGCC CTAAACAGCAATGGAC CTACCTCACAATGGAC CTCAAAAGCAATGGAC CTCAACAACAATGGAC CTCAACACCAATGGAC CTCAACAGCAAAGGAC CTCAACAGCAAGGGAC CTCAACAGCAATCGAC CTCAACAGCAATGCAC CTCAACAGCAATGGAA CTCAACAGCAATGGAC CTCAACAGCAATGGAG CTCAACAGCAATGGAT CTCAACAGCAATGGCC CTCAACAGCAATGGGC CTCAACAGCAATGGTC CTCAACAGCAATGTAC CTCAACAGCAATTGAC CTCAACAGCATTGGAC CTCAACAGCCATGGAC CTCAACAGCTATGGAC CTCAACAGGAATGGAC CTCAACATCAATGGAC CTCAACCGCAATGGAC CTCAACTGCAATGGAC CTCAAGAGCAATGGAC CTCACCAGCAATGGAC CTCATCAGCAATGGAC CTCCACAGCAATGGAC CTCCACAGCAATGGCC CTCGACAGCAATGGAC CTCTACAGCAATGGAC CTCTACAGCAATGGCC CTGAACAGCAATGGAC CTGGAACCCAATGGAC CTGGAACCCCATCCAA GAAGAGTTCAATGGAC GAATGTCTCAAGAGGT GAGAGACGCAATGGAC GAGCCGTTCAAGAGGT GCAAGTCTCAAGAGGT GCAGAGTTCAATGGAC GCATATCTCAAGAGGT GCATCTCTCAAGAGGT GCATGACTCAAGAGGT GCATGGCTCAAGAGGT GCATGTATCAAGAGGT GCATGTCACAAGAGGT GCATGTCCCAAGAGGT GCATGTCGCAAGAGGT GCATGTCTCAAAAGGT GCATGTCTCAACAGGT GCATGTCTCAAGAAGT GCATGTCTCAAGACGT GCATGTCTCAAGAGCT GCATGTCTCAAGAGGA GCATGTCTCAAGAGGG GCATGTCTCAAGAGGT GCATGTCTCAAGAGTT GCATGTCTCAAGATGT GCATGTCTCAAGCGGT GCATGTCTCAAGTGGT GCATGTCTCAATAGGT GCATGTCTCAGGAGGT GCATGTCTCATGAGGT GCATGTCTCTAGAGGT GCATGTCTGAAGAGGT GCATGTCTTAAGAGGT GCATGTGTCAAGAGGT GCATTTCTCAAGAGGT GCCAAGTCCAAGAGGT GCCTGTCTCAAGAGGT GCCTTGCTCAATGGAC GCTCTCAACAATGGAC GCTTGTCTCAAGAGGT GCTTGTCTCAAGCGGT GGAAAGTTCAATGGAC GGACAGTTCAATGGAC GGACCAAGCAATGGAC GGACTCAACAATGGAC GGAGAATTCAATGGAC GGAGACTTCAATGGAC GGAGAGATCAATGGAC GGAGAGGTCAATGGAC GGAGAGGTCAATGGTC GGAGAGTACAATGGAC GGAGAGTACAATGGCC GGAGAGTGCAATGGAC GGAGAGTTAAATGGAC GGAGAGTTCAAAGGAC GGAGAGTTCAAGGGAC GGAGAGTTCAATAGAC GGAGAGTTCAATCGAC GGAGAGTTCAATGAAC GGAGAGTTCAATGCAC GGAGAGTTCAATGGAA GGAGAGTTCAATGGAC GGAGAGTTCAATGGAG GGAGAGTTCAATGGCC GGAGAGTTCAATGGGC GGAGAGTTCAATGGTC GGAGAGTTCAATGTAC GGAGAGTTCAATTGAC GGAGAGTTCATTGGAC GGAGAGTTCCATGGAC GGAGAGTTCGATGGAC GGAGAGTTCTATGGAC GGAGAGTTGAATGGAC GGAGCGTTCAATGGAC GGAGCGTTCAATGGCC GGAGGGTTCAATGGAC GGAGTGTTCAATGGAC GGATAGTTCAATGGAC GGATGTCTCAAGAGGT GGCGAGTTCAATGGAC GGGCTCAACAATGGAC GGGGAGTTCAATGGAC GGTATCAACAATGGAC GGTCACAACAATGGAC GGTCGCAACAATGGAC GGTCTAAACAATGGAC GGTCTCAAAAATGGAC GGTCTCAACAAAGGAC GGTCTCAACAATAGAC GGTCTCAACAATCGAC GGTCTCAACAATGAAC GGTCTCAACAATGGAA GGTCTCAACAATGGAC GGTCTCAACAATGGAG GGTCTCAACAATGGCC GGTCTCAACAATGGGC GGTCTCAACAATGGTC GGTCTCAACAATTGAC GGTCTCAACATTGGAC GGTCTCAACCATGGAC GGTCTCAACTATGGAC GGTCTCACCAATGGAC GGTCTCATCAATGGAC GGTCTCCACAATGGAC GGTCTCTACAATGGAC GGTGAGTTCAATGGAC GGTGAGTTCAATGGCC GGTGTCAACAATGGAC GTGGAACCCAATGGAC GTGGAACCCAATGGCC GTGGAACCCCATCCAA TAACCAAGCAATGGAC TACAAGTCCAAGAGGT TACAGATGCAATGGAC TACCAATGCAATGGAC TACCCATGCAATGGAC TACCGAAGCAATGGAC TACCGAGGCAATGGAC TACCGATACAATGGAC TACCGATCCAATGGAC TACCGATGCAAAGGAC TACCGATGCAAGGGAC TACCGATGCAATAGAC TACCGATGCAATCGAC TACCGATGCAATGAAC TACCGATGCAATGCAC TACCGATGCAATGGAC TACCGATGCAATGGAG TACCGATGCAATGGAT TACCGATGCAATGGCC TACCGATGCAATGGGC TACCGATGCAATGGTC TACCGATGCAATGTAC TACCGATGCAATTGAC TACCGATGCATTGGAC TACCGATGCCATGGAC TACCGATGCTATGGAC TACCGATGGAATGGAC TACCGCTGCAATGGAC TACCGTTGCAATGGAC TACGGATGCAATGGAC TACTGATGCAATGGAC TACTTGCTCAATGGAC TAGAGACGCAATGGAC TAGCCGTTCAAGAGGT TAGCGATGCAATGGAC TAGGAACCCAATGGAC TAGGAACCCCATCCAA TCAAAGTCCAAGAGGT TCACCAAGCAATGGAC TCATTGCTCAATGGAC TCATTGCTCAATGGCC TCCAAATCCAAGAGGT TCCAACTCCAAGAGGT TCCAAGACCAAGAGGT TCCAAGCCCAAGAGGT TCCAAGGCCAAGAGGT TCCAAGTACAAGAGGT TCCAAGTCAAAGAGGT TCCAAGTCCAAAAGGT TCCAAGTCCAACAGGT TCCAAGTCCAAGACGT TCCAAGTCCAAGAGAT TCCAAGTCCAAGAGCT TCCAAGTCCAAGAGGA TCCAAGTCCAAGAGGC TCCAAGTCCAAGAGGG TCCAAGTCCAAGAGGT TCCAAGTCCAAGAGTT TCCAAGTCCAAGATGT TCCAAGTCCAAGCGGT TCCAAGTCCAAGTGGT TCCAAGTCCAATAGGT TCCAAGTCCATGAGGT TCCAAGTCCCAGAGGT TCCAAGTCCGAGAGGT TCCAAGTCCTAGAGGT TCCAAGTCGAAGAGGT TCCAAGTGCAAGAGGT TCCAAGTTCAAGAGGT TCCAATTCCAAGAGGT TCCACGTCCAAGAGGT TCCAGGTCCAAGAGGT TCCATGCTCAATGGAC TCCATGCTCAATGGCC TCCATGTCCAAGAGGT TCCCAGTCCAAGAGGT TCCGAGTCCAAGAGGT TCCGTGCTCAATGGAC TCCTAGCTCAATGGAC TCCTAGTCCAAGAGGT TCCTTACTCAATGGAC TCCTTCCTCAATGGAC TCCTTGATCAATGGAC TCCTTGCACAATGGAC TCCTTGCCCAATGGAC TCCTTGCGCAATGGAC TCCTTGCTCAAAGGAC TCCTTGCTCAAGGGAC TCCTTGCTCAATAGAC TCCTTGCTCAATCGAC TCCTTGCTCAATGAAC TCCTTGCTCAATGCAC TCCTTGCTCAATGGAA TCCTTGCTCAATGGAC TCCTTGCTCAATGGAG TCCTTGCTCAATGGCC TCCTTGCTCAATGGGC TCCTTGCTCAATGGTC TCCTTGCTCAATGTAC TCCTTGCTCAATTGAC TCCTTGCTCATTGGAC TCCTTGCTCCATGGAC TCCTTGCTCGATGGAC TCCTTGCTCTATGGAC TCCTTGCTGAATGGAC TCCTTGCTTAATGGAC TCCTTGGTCAATGGAC TCCTTTCTCAATGGAC TCGAAGTCCAAGAGGT TCGGAACCCAATGGAC TCGGAACCCCATCCAA TCGTTGCTCAATGGAC TCTAAGTCCAAGAGGT TGAACAAGCAATGGAC TGACAAAGCAATGGAC TGACCAAACAATGGAC TGACCAACCAATGGAC TGACCAAGCAAAGGAC TGACCAAGCAAGGGAC TGACCAAGCAATAGAC TGACCAAGCAATCGAC TGACCAAGCAATGAAC TGACCAAGCAATGCAC TGACCAAGCAATGGAA TGACCAAGCAATGGAC TGACCAAGCAATGGAG TGACCAAGCAATGGAT TGACCAAGCAATGGCC TGACCAAGCAATGGGC TGACCAAGCAATGGTC TGACCAAGCAATGTAC TGACCAAGCAATTGAC TGACCAAGCATTGGAC TGACCAAGCCATGGAC TGACCAAGCTATGGAC TGACCAAGTAATGGAC TGACCAATCAATGGAC TGACCACGCAATGGAC TGACCAGGCAATGGAC TGACCATGCAATGGAC TGACCATGCAATGGCC TGACCCAGCAATGGAC TGACCTAGCAATGGAC TGACGAAGCAATGGAC TGAGAGTTCAATGGAC TGAGCAAGCAATGGAC TGCAAGTCCAAGAGGT TGCCCAAGCAATGGAC TGCCCAAGCAATGGCC TGCCCAAGCAATGGTC TGCCCAAGCATTGGAC TGCCGATGCAATGGAC TGCTTGCTCAATGGAC TGGCCAAGCAATGGAC TGGGAACCCAATGGAC TGGGAACCCCATCCAA TGTCCAAGCAATGGAC TTAGAACCCAATGGAC TTCAAGTCCAAGAGGT TTCCGATGCAATGGAC TTCGAACCCAATGGAC TTCGAACCCCATCCAA TTCTTGCTCAATGGAC TTGAAACCCAATGGAC TTGAAACCCCATCCAA TTGCAACCCAATGGAC TTGCAACCCCATCCAA TTGGAAACCAATGGAC TTGGAAACCCATCCAA TTGGAACACAATGGAC TTGGAACACCATCCAA TTGGAACCACATCCAA TTGGAACCCAAAGGAC TTGGAACCCAAGGGAC TTGGAACCCAATAGAC TTGGAACCCAATCCAA TTGGAACCCAATCGAC TTGGAACCCAATGAAC TTGGAACCCAATGCAC TTGGAACCCAATGGAA TTGGAACCCAATGGAC TTGGAACCCAATGGAG TTGGAACCCAATGGCC TTGGAACCCAATGGGC TTGGAACCCAATGGTC TTGGAACCCAATGTAC TTGGAACCCAATTGAC TTGGAACCCATTGGAC TTGGAACCCCAACCAA TTGGAACCCCATACAA TTGGAACCCCATCAAA TTGGAACCCCATCCAA TTGGAACCCCATCCAG TTGGAACCCCATCCAT TTGGAACCCCATCCCA TTGGAACCCCATCCTA TTGGAACCCCATGGAC TTGGAACCCCCTCCAA TTGGAACCCCGTCCAA TTGGAACCCCTTCCAA TTGGAACCCGATCCAA TTGGAACCCTATGGAC TTGGAACCGAATGGAC TTGGAACCGCATCCAA TTGGAACCTAATGGAC TTGGAACGCAATGGAC TTGGAAGCCAATGGAC TTGGACCCCAATGGAC TTGGACCCCAATGGCC TTGGACCCCCATCCAA TTGGAGCCCAATGGAC TTGGAGCCCCATCCAA TTGGATCCCAATGGAC TTGGATCCCCATCCAA TTGGCACCCAATGGAC TTGGCACCCAATGGCC TTGGCACCCAATGGTC TTGGCACCCCATCCAA TTGGGACCCAATGGAC TTGGGACCCCATCCAA TTGGTACCCAATGGAC TTGGTACCCCATCCAA TTTGAACCCAATGGAC
