What is the Cell Ranger VDJ Pipeline?
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The cellranger (v9.0.0) vdj pipeline can be used to analyze sequencing data produced from Chromium Single Cell 5' V(D)J libraries. It takes FASTQ files from 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.