Loading .gitattributes +2 −0 Original line number Diff line number Diff line Loading @@ -70,3 +70,5 @@ test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R2_001.fastq.gz filter=l test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_I1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text whitelists/KAPA_UDI_Index2_i5.txt filter=lfs diff=lfs merge=lfs -text whitelists/KAPA_UDI_Index1_i7.txt filter=lfs diff=lfs merge=lfs -text README.Rmd +7 −0 Original line number Diff line number Diff line Loading @@ -166,6 +166,10 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De - 10x Genomics version 3 (16 bp barcode, 12 bp UMI): 10x-v3, chromium-v3 - Aligent Bravo B (16 bp barcode, No UMI): aligent, bravo - BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody - C1 - C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1 - C1 CAGE (16 bp, No UMI): c1-cage - C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq - CEL-Seq - CEL-Seq (8 bp barcode, 4 bp UMI): celseq - CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2 Loading Loading @@ -1104,6 +1108,9 @@ Mandatory arguments to long options are mandatory for short options too. 10x Genomics version 3 (16 bp barcode, 12 bp UMI): 10x-v3, chromium-v3 Aligent Bravo B (16 bp barcode, No UMI): aligent, bravo BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1 C1 CAGE (16 bp, No UMI): c1-cage C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq CEL-Seq (8 bp barcode, 4 bp UMI): celseq CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2 Drop-Seq (12 bp barcode, 8 bp UMI): dropseq Loading README.html +9 −0 Original line number Diff line number Diff line Loading @@ -48,6 +48,12 @@ </ul></li> <li>Aligent Bravo B (16 bp barcode, No UMI): aligent, bravo</li> <li>BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody</li> <li>C1 <ul> <li>C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1</li> <li>C1 CAGE (16 bp, No UMI): c1-cage</li> <li>C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq</li> </ul></li> <li>CEL-Seq <ul> <li>CEL-Seq (8 bp barcode, 4 bp UMI): celseq</li> Loading Loading @@ -540,6 +546,9 @@ Mandatory arguments to long options are mandatory for short options too. 10x Genomics version 3 (16 bp barcode, 12 bp UMI): 10x-v3, chromium-v3 Aligent Bravo B (16 bp barcode, No UMI): aligent, bravo BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1 C1 CAGE (16 bp, No UMI): c1-cage C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq CEL-Seq (8 bp barcode, 4 bp UMI): celseq CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2 Drop-Seq (12 bp barcode, 8 bp UMI): dropseq Loading README.md +7 −0 Original line number Diff line number Diff line Loading @@ -166,6 +166,10 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De - 10x Genomics version 3 (16 bp barcode, 12 bp UMI): 10x-v3, chromium-v3 - Aligent Bravo B (16 bp barcode, No UMI): aligent, bravo - BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody - C1 - C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1 - C1 CAGE (16 bp, No UMI): c1-cage - C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq - CEL-Seq - CEL-Seq (8 bp barcode, 4 bp UMI): celseq - CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2 Loading Loading @@ -1104,6 +1108,9 @@ Mandatory arguments to long options are mandatory for short options too. 10x Genomics version 3 (16 bp barcode, 12 bp UMI): 10x-v3, chromium-v3 Aligent Bravo B (16 bp barcode, No UMI): aligent, bravo BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1 C1 CAGE (16 bp, No UMI): c1-cage C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq CEL-Seq (8 bp barcode, 4 bp UMI): celseq CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2 Drop-Seq (12 bp barcode, 8 bp UMI): dropseq Loading man/launch_universc.sh +3 −0 Original line number Diff line number Diff line Loading @@ -200,6 +200,9 @@ Provides a conversion script to run multiple technologies and custom libraries w BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody CEL-Seq (8 bp barcode, 4 bp UMI): celseq CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2 C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1 C1 CAGE (16 bp, No UMI): c1-cage C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq Drop-Seq (12 bp barcode, 8 bp UMI): dropseq ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2 ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom Loading Loading
.gitattributes +2 −0 Original line number Diff line number Diff line Loading @@ -70,3 +70,5 @@ test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L001_R2_001.fastq.gz filter=l test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_I1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text whitelists/KAPA_UDI_Index2_i5.txt filter=lfs diff=lfs merge=lfs -text whitelists/KAPA_UDI_Index1_i7.txt filter=lfs diff=lfs merge=lfs -text
README.Rmd +7 −0 Original line number Diff line number Diff line Loading @@ -166,6 +166,10 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De - 10x Genomics version 3 (16 bp barcode, 12 bp UMI): 10x-v3, chromium-v3 - Aligent Bravo B (16 bp barcode, No UMI): aligent, bravo - BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody - C1 - C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1 - C1 CAGE (16 bp, No UMI): c1-cage - C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq - CEL-Seq - CEL-Seq (8 bp barcode, 4 bp UMI): celseq - CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2 Loading Loading @@ -1104,6 +1108,9 @@ Mandatory arguments to long options are mandatory for short options too. 10x Genomics version 3 (16 bp barcode, 12 bp UMI): 10x-v3, chromium-v3 Aligent Bravo B (16 bp barcode, No UMI): aligent, bravo BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1 C1 CAGE (16 bp, No UMI): c1-cage C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq CEL-Seq (8 bp barcode, 4 bp UMI): celseq CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2 Drop-Seq (12 bp barcode, 8 bp UMI): dropseq Loading
README.html +9 −0 Original line number Diff line number Diff line Loading @@ -48,6 +48,12 @@ </ul></li> <li>Aligent Bravo B (16 bp barcode, No UMI): aligent, bravo</li> <li>BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody</li> <li>C1 <ul> <li>C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1</li> <li>C1 CAGE (16 bp, No UMI): c1-cage</li> <li>C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq</li> </ul></li> <li>CEL-Seq <ul> <li>CEL-Seq (8 bp barcode, 4 bp UMI): celseq</li> Loading Loading @@ -540,6 +546,9 @@ Mandatory arguments to long options are mandatory for short options too. 10x Genomics version 3 (16 bp barcode, 12 bp UMI): 10x-v3, chromium-v3 Aligent Bravo B (16 bp barcode, No UMI): aligent, bravo BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1 C1 CAGE (16 bp, No UMI): c1-cage C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq CEL-Seq (8 bp barcode, 4 bp UMI): celseq CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2 Drop-Seq (12 bp barcode, 8 bp UMI): dropseq Loading
README.md +7 −0 Original line number Diff line number Diff line Loading @@ -166,6 +166,10 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De - 10x Genomics version 3 (16 bp barcode, 12 bp UMI): 10x-v3, chromium-v3 - Aligent Bravo B (16 bp barcode, No UMI): aligent, bravo - BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody - C1 - C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1 - C1 CAGE (16 bp, No UMI): c1-cage - C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq - CEL-Seq - CEL-Seq (8 bp barcode, 4 bp UMI): celseq - CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2 Loading Loading @@ -1104,6 +1108,9 @@ Mandatory arguments to long options are mandatory for short options too. 10x Genomics version 3 (16 bp barcode, 12 bp UMI): 10x-v3, chromium-v3 Aligent Bravo B (16 bp barcode, No UMI): aligent, bravo BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1 C1 CAGE (16 bp, No UMI): c1-cage C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq CEL-Seq (8 bp barcode, 4 bp UMI): celseq CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2 Drop-Seq (12 bp barcode, 8 bp UMI): dropseq Loading
man/launch_universc.sh +3 −0 Original line number Diff line number Diff line Loading @@ -200,6 +200,9 @@ Provides a conversion script to run multiple technologies and custom libraries w BD Rhapsody (27 bp barcode, 8 bp UMI): bd-rhapsody CEL-Seq (8 bp barcode, 4 bp UMI): celseq CEL-Seq2 (6 bp UMI, 6 bp barcode): celseq2 C1 Fluidigm (16 bp barcode, No UMI): c1, fluidgm-c1 C1 CAGE (16 bp, No UMI): c1-cage C1 RamDA-Seq (16 bp, No UMI): c1-ramda-seq Drop-Seq (12 bp barcode, 8 bp UMI): dropseq ICELL8 version 2 (11 bp barcode, No UMI): icell8-non-umi, icell8-v2 ICELL8 version 3 (11 bp barcode, 14 bp UMI): icell8 or custom Loading
