Loading README.Rmd +5 −1 Original line number Diff line number Diff line Loading @@ -121,6 +121,8 @@ avoid causing problems with existing runs). Multiple samples of the same technol - inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1 - inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2 - inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 - MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1 - MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2 - Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384 - Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536 - Sci-Seq (8bp UMI, 10bp barcode): sciseq Loading Loading @@ -809,6 +811,8 @@ Mandatory arguments to long options are mandatory for short options too. inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1 inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2 inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1 MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2 Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384 Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536 Sci-Seq (8bp UMI, 10bp barcode): sciseq Loading README.md +5 −1 Original line number Diff line number Diff line Loading @@ -121,6 +121,8 @@ avoid causing problems with existing runs). Multiple samples of the same technol - inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1 - inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2 - inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 - MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1 - MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2 - Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384 - Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536 - Sci-Seq (8bp UMI, 10bp barcode): sciseq Loading Loading @@ -809,6 +811,8 @@ Mandatory arguments to long options are mandatory for short options too. inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1 inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2 inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1 MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2 Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384 Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536 Sci-Seq (8bp UMI, 10bp barcode): sciseq Loading launch_universc.sh +14 −0 Original line number Diff line number Diff line Loading @@ -156,6 +156,8 @@ Mandatory arguments to long options are mandatory for short options too. inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1 inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2 inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1 MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2 Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384 Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536 Sci-Seq (8bp UMI, 10bp barcode): sciseq Loading Loading @@ -545,6 +547,10 @@ elif [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrops-v2" ]] | technology="indrop-v2" elif [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "indrops-v3" ]] || [[ "$technology" == "indropv3" ]] || [[ "$technology" == "indropsv3" ]] || [[ "$technology" == "1cellbio-v3" ]] || [[ "$technology" == "1cellbiov3" ]]; then technology="indrop-v3" elif [[ "$technology" == "marsseq" ]] || [[ "$technology" == "mars-seq" ]] || [[ "$technology" == "marsseq-v1" ]] || [[ "$technology" == "mars-seq-v1" ]] || [[ "$technology" == "marsseqv1" ]] || [[ "$technology" == "mars-seqv1" ]]; then technology="marsseq-v1" elif [[ "$technology" == "marsseq2" ]] || [[ "$technology" == "mars-seq2" ]] || [[ "$technology" == "marsseq-v2" ]] || [[ "$technology" == "mars-seq-v2" ]] || [[ "$technology" == "marsseqv2" ]] || [[ "$technology" == "mars-seqv2" ]]; then technology="marsseq-v2" elif [[ "$technology" == "quartz-seq2-384" ]] || [[ "$technology" == "quartzseq2-384" ]] || [[ "$technology" == "quartz-seq2-v3.1" ]] || [[ "$technology" == "quartzseq2-v3.1" ]] || [[ "$technology" == "quartzseq2v3.1" ]]; then technology="quartz-seq2-384" elif [[ "$technology" == "quartz-seq2-1536" ]] || [[ "$technology" == "quartzseq2-1536" ]] || [[ "$technology" == "quartz-seq2-v3.2" ]] || [[ "$technology" == "quartzseq2-v3.2" ]] || [[ "$technology" == "quartzseq2v3.2" ]]; then Loading Loading @@ -640,6 +646,14 @@ if [[ "$technology" == "indrop-v3" ]]; then barcodelength=11 umilength=6 minlength=8 elif [[ "$technology" == "marsseq-v1" ]]; then barcodelength=6 umilength=10 minlength=6 elif [[ "$technology" == "marsseq-v2" ]]; then barcodelength=7 umilength=8 minlength=7 elif [[ "$technology" == "quartz-seq2-384" ]]; then barcodelength=14 umilength=8 Loading man/convert.sh +2 −0 Original line number Diff line number Diff line Loading @@ -195,6 +195,8 @@ Provides a conversion script to run multiple technologies and custom libraries w inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1 inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2 inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1 MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2 Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384 Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536 Sci-Seq (8bp UMI, 10bp barcode): sciseq Loading Loading
README.Rmd +5 −1 Original line number Diff line number Diff line Loading @@ -121,6 +121,8 @@ avoid causing problems with existing runs). Multiple samples of the same technol - inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1 - inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2 - inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 - MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1 - MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2 - Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384 - Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536 - Sci-Seq (8bp UMI, 10bp barcode): sciseq Loading Loading @@ -809,6 +811,8 @@ Mandatory arguments to long options are mandatory for short options too. inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1 inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2 inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1 MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2 Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384 Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536 Sci-Seq (8bp UMI, 10bp barcode): sciseq Loading
README.md +5 −1 Original line number Diff line number Diff line Loading @@ -121,6 +121,8 @@ avoid causing problems with existing runs). Multiple samples of the same technol - inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1 - inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2 - inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 - MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1 - MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2 - Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384 - Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536 - Sci-Seq (8bp UMI, 10bp barcode): sciseq Loading Loading @@ -809,6 +811,8 @@ Mandatory arguments to long options are mandatory for short options too. inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1 inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2 inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1 MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2 Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384 Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536 Sci-Seq (8bp UMI, 10bp barcode): sciseq Loading
launch_universc.sh +14 −0 Original line number Diff line number Diff line Loading @@ -156,6 +156,8 @@ Mandatory arguments to long options are mandatory for short options too. inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1 inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2 inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1 MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2 Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384 Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536 Sci-Seq (8bp UMI, 10bp barcode): sciseq Loading Loading @@ -545,6 +547,10 @@ elif [[ "$technology" == "indrop-v2" ]] || [[ "$technology" == "indrops-v2" ]] | technology="indrop-v2" elif [[ "$technology" == "indrop-v3" ]] || [[ "$technology" == "indrops-v3" ]] || [[ "$technology" == "indropv3" ]] || [[ "$technology" == "indropsv3" ]] || [[ "$technology" == "1cellbio-v3" ]] || [[ "$technology" == "1cellbiov3" ]]; then technology="indrop-v3" elif [[ "$technology" == "marsseq" ]] || [[ "$technology" == "mars-seq" ]] || [[ "$technology" == "marsseq-v1" ]] || [[ "$technology" == "mars-seq-v1" ]] || [[ "$technology" == "marsseqv1" ]] || [[ "$technology" == "mars-seqv1" ]]; then technology="marsseq-v1" elif [[ "$technology" == "marsseq2" ]] || [[ "$technology" == "mars-seq2" ]] || [[ "$technology" == "marsseq-v2" ]] || [[ "$technology" == "mars-seq-v2" ]] || [[ "$technology" == "marsseqv2" ]] || [[ "$technology" == "mars-seqv2" ]]; then technology="marsseq-v2" elif [[ "$technology" == "quartz-seq2-384" ]] || [[ "$technology" == "quartzseq2-384" ]] || [[ "$technology" == "quartz-seq2-v3.1" ]] || [[ "$technology" == "quartzseq2-v3.1" ]] || [[ "$technology" == "quartzseq2v3.1" ]]; then technology="quartz-seq2-384" elif [[ "$technology" == "quartz-seq2-1536" ]] || [[ "$technology" == "quartzseq2-1536" ]] || [[ "$technology" == "quartz-seq2-v3.2" ]] || [[ "$technology" == "quartzseq2-v3.2" ]] || [[ "$technology" == "quartzseq2v3.2" ]]; then Loading Loading @@ -640,6 +646,14 @@ if [[ "$technology" == "indrop-v3" ]]; then barcodelength=11 umilength=6 minlength=8 elif [[ "$technology" == "marsseq-v1" ]]; then barcodelength=6 umilength=10 minlength=6 elif [[ "$technology" == "marsseq-v2" ]]; then barcodelength=7 umilength=8 minlength=7 elif [[ "$technology" == "quartz-seq2-384" ]]; then barcodelength=14 umilength=8 Loading
man/convert.sh +2 −0 Original line number Diff line number Diff line Loading @@ -195,6 +195,8 @@ Provides a conversion script to run multiple technologies and custom libraries w inDrops version 1 (19bp barcode, 6bp UMI): indrops-v1, 1cellbio-v1 inDrops version 2 (19bp barcode, 6bp UMI): indrops-v2, 1cellbio-v2 inDrops version 3 (8bp barcode, 6bp UMI): indrops-v3, 1cellbio-v3 MARS-Seq (6bp barcode, 10bp UMI): marsseq, marsseq-v1 MARS-Seq2 (7bp barcode, 8bp UMI): marsseq2, marsseq-v2 Quartz-Seq2 (14bp barcode, 8bp UMI): quartzseq2-384 Quartz-Seq2 (15bp barcode, 8bp UMI): quartzseq2-1536 Sci-Seq (8bp UMI, 10bp barcode): sciseq Loading
