Answer: With Cell Ranger v5"/> Cellranger multi vdj --denovo Run in reference-free mode (do not use annotations). It takes FASTQ files from cellranger mkfastq or bcl2fastq for V (D)J libraries and performs sequence assembly and paired clonotype calling. 4: Find and record the number of cells called per sample Step 1. Web. The structure and contents of this tab are similar to the VDJ-T tab. Following a series of checks to validate input arguments, cellranger multi pipeline stages will begin to run:. Web. Check out the cellranger multi pipeline page to analyze both libraries together.