modules/cellranger_vdj
Module to use Cell Ranger’s pipelines analyze sequencing data produced from Chromium Single Cell Immune Profiling.
alignvdjreferenceimmunoprofilingsingle-cellcellranger
Description
Module to use Cell Ranger’s pipelines analyze sequencing data produced from Chromium Single Cell Immune Profiling.
Tools
cellranger 10X Genomics EULA
Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe V(D)J Browser.