Cell Ranger7.1 (latest), printed on 06/06/2023
Cell Ranger provides a set of analysis pipelines for processing Chromium Next GEM Single Cell Immune Profiling data to align reads, generate Feature Barcode (FB) matrices, perform clustering and secondary analyses, and more.
Start by choosing a computing option to set up and run Cell Ranger.
Cell Ranger pipelines require FASTQ files. If needed, convert raw sequence BCL files to FASTQ format with cellranger mkfastq (alternatively, use bcl2fastq or BCL Convert).
Conduct primary analysis:
|Documentation by library type||Cell Ranger pipeline|
|Gene Expression only||count|
|Antibody Capture ± Gene Expression||count|
|CRISPR (FB) + Gene Expression||count|
|Gene Expression + V(D)J ± FB||multi|
|Gene Expression + V(D)J + Antigen Capture (BEAM) ± Antibody Capture||multi|
For assistance with a specific library combination not documented here, please contact [email protected]