Loading launch_universc.sh +1 −1 Original line number Diff line number Diff line Loading @@ -74,7 +74,7 @@ Mandatory arguments to long options are mandatory for short options too. 10x Genomics (16bp barcode, 10bp UMI): 10x, chromium (v2 or v3 automatically detected) CEL-Seq (8bp barcode, 4bp UMI): celseq CEL-Seq2 (6bp UMI, 6bp barcode): celseq2 Drop-Seq (12bp barcode, 8pm UMI): nadia, dropseq Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq iCell8 version 3 (11bp barcode, 14bp UMI): icell8 or custom inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1 inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2 Loading test/shared/cellranger-tiny-fastq/README.md 0 → 100644 +21 −0 Original line number Diff line number Diff line ## Test data for Chromium technique (10x settings) ### Beads supplied by 10x Genomics (16bp barcode, 10bp UMI) Citation: Zheng et al (2017) Massively parallel digital transcriptional profiling of single cells. Nat Commun. 2017; 8: 14049 doi: 10.1038/ncomms14049 ## Data source Test data from cellranger version 2.1.0 and 3.0.2 https://github.com/10XGenomics/cellranger http://support.10xgenomics.com/single-cell/datasets SRA Archive: Study Accession: SRP073767 https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP073767 ## Data preparations Regions mapping to HUMAN_21:9825832-48085036 GRCh38 (hg38) Tiny test dataset https://github.com/10XGenomics/single-cell-3prime-paper test/shared/dropseq-test/README.md +2 −2 Original line number Diff line number Diff line ## Test data for Drop-Seq technique (Nadia settings) ### Beads supplied by ChemGenes (12bp barcode, 8pm UMI) ### Beads supplied by ChemGenes (12bp barcode, 8bp UMI) Citation: Macosko et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 161(5):1202-1214. Loading @@ -18,6 +18,6 @@ https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1629192 ## Data preparations Filtered for regions mapping to HUMAN_21:9825832-48085036 GRCh38 (hg38) f Filtered for regions mapping to HUMAN_21:9825832-48085036 GRCh38 (hg38) Matched by fastq_pair (https://github.com/linsalrob/fastq-pair) Loading
launch_universc.sh +1 −1 Original line number Diff line number Diff line Loading @@ -74,7 +74,7 @@ Mandatory arguments to long options are mandatory for short options too. 10x Genomics (16bp barcode, 10bp UMI): 10x, chromium (v2 or v3 automatically detected) CEL-Seq (8bp barcode, 4bp UMI): celseq CEL-Seq2 (6bp UMI, 6bp barcode): celseq2 Drop-Seq (12bp barcode, 8pm UMI): nadia, dropseq Drop-Seq (12bp barcode, 8bp UMI): nadia, dropseq iCell8 version 3 (11bp barcode, 14bp UMI): icell8 or custom inDrops version 1 (19bp barcode, 8bp UMI): indrops-v1, 1cellbio-v1 inDrops version 2 (19bp barcode, 8bp UMI): indrops-v2, 1cellbio-v2 Loading
test/shared/cellranger-tiny-fastq/README.md 0 → 100644 +21 −0 Original line number Diff line number Diff line ## Test data for Chromium technique (10x settings) ### Beads supplied by 10x Genomics (16bp barcode, 10bp UMI) Citation: Zheng et al (2017) Massively parallel digital transcriptional profiling of single cells. Nat Commun. 2017; 8: 14049 doi: 10.1038/ncomms14049 ## Data source Test data from cellranger version 2.1.0 and 3.0.2 https://github.com/10XGenomics/cellranger http://support.10xgenomics.com/single-cell/datasets SRA Archive: Study Accession: SRP073767 https://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP073767 ## Data preparations Regions mapping to HUMAN_21:9825832-48085036 GRCh38 (hg38) Tiny test dataset https://github.com/10XGenomics/single-cell-3prime-paper
test/shared/dropseq-test/README.md +2 −2 Original line number Diff line number Diff line ## Test data for Drop-Seq technique (Nadia settings) ### Beads supplied by ChemGenes (12bp barcode, 8pm UMI) ### Beads supplied by ChemGenes (12bp barcode, 8bp UMI) Citation: Macosko et al (2015) Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell 161(5):1202-1214. Loading @@ -18,6 +18,6 @@ https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1629192 ## Data preparations Filtered for regions mapping to HUMAN_21:9825832-48085036 GRCh38 (hg38) f Filtered for regions mapping to HUMAN_21:9825832-48085036 GRCh38 (hg38) Matched by fastq_pair (https://github.com/linsalrob/fastq-pair)
