Dockerized Cell Ranger ARC v2.0.2
SCING (Single-Cell pIpeliNe Garden; pronounced as "sing" /siŋ/) is required for smooth and uninteruppted build process (e.g. CI/CD). For setup, please refer to this page. All the instructions below is given under the assumption that you have already configured SCING in your environment.
SCING installation is required.
conda activate scing
./build.shconda activate scing
./push.sh$ docker run -it --rm cellranger-arc:2.0.2
cellranger-arc cellranger-arc-2.0.2
Process 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression data
USAGE:
cellranger-arc <SUBCOMMAND>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
SUBCOMMANDS:
count Count ATAC and gene expression reads from a single library
mkfastq Run bcl2fastq on Single Cell Multiome ATAC + Gene Expression sequencing data
mkref Create a cellranger-arc-compatible reference package
aggr Aggregate data from multiple `cellranger-arc count` runs
reanalyze Re-run secondary analysis (dimensionality reduction, clustering, feature
linkage etc.) on a completed `cellranger-arc count` or `cellranger-arc aggr`
run
testrun Run a tiny cellranger-arc count pipeline to verify software integrity
mkgtf Filter a GTF file by attribute prior to creating a 10x reference
upload Upload analysis logs to 10x Genomics support
sitecheck Collect linux system configuration information
help Prints this message or the help of the given subcommand(s)
- GEX barcode list:
737K-arc-gex-v1.txt.gz - ATAC barcode list:
737K-arc-atac-v1.txt.gz
The two files have the same number of lines (modulo new lines). The line-by-line correspondence between barcodes in the two files gives you the bijective map between the GEX barcode and ATAC barcode in each gel bead. For instance, the gex barcode on line 34 and the atac barcode on line 34 are part of the same gel bead.