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  1. 10X Genomics
  2. Single Cell Immune Profiling
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Software

  • What are the major updates in Cell Ranger v7.1 that impacts V(D)J data?
  • Building a custom reference for V(D)J using IMGT tool
  • Loupe Browser investigation for GEX + V(D)J data for differences in cell numbers
  • Web summary metrics for V(D)J Troubleshooting
  • Usage of Cell Ranger VDJ denovo mode
  • How to run Cell Ranger for the same 5' GEX library sequenced with 150x150 and 26x98 configurations?
  • How can I combine and compare data from 5’v1/v1.1 chemistry with 5’v2 chemistry?
  • Is there a minimum number of Cell Surface Proteins that can be analyzed with Cell Ranger
  • Can I run the VDJ pipeline for humanized mouse samples
  • How can I get the sequence for each gene segment in an Ig or TCR chain
  • Why does Loupe Cell Browser show "The VDJ file may not be related to this gene expression dataset" when I tried to load my matched VDJ data?
  • Why do some clonotypes only have one productive chain?
  • What should I do when I get more than 1 chain of same type in the same cell?
  • Where can I find isotype information for V(D)J libraries?
  • Can I detect IgA1 and IgA2 in the Single Cell V(D)J assay?
  • Error in demultiplexing libraries indexed with 10x Chromium i7 Multiplex Kit and i7 Multiplex Kit N plates that were sequenced in the same run
  • How can I pick up SNPs and other mutations in the V(D)J pipeline?
  • How can I combine V(D)J data for multiple libraries with Cell Ranger?
  • Can I identify differentially expressed genes between cells in two different clonotypes?
  • Is the amino acid sequence for the full V(D)J contig available?
  • Are the V(D)J and gene expression references interchangeable?
  • What genes and criteria were used for clustering the lung cancer data in the 5' gene expression and V(D)J integrated tutorial?
  • Why is a TRB chain paired with a TRA in clonotype1 and alone in clonotype2?
  • Why is the D gene annotation missing in several chains in the TCR or BCR data?
  • What is the source of 'Multi' chains in the contig_annotations.csv files?
  • If cells have the same CDR3, but different genes, will they be called as different clonotypes?
  • Can we tell which barcodes (GEMs) contain more than one cell for V(D)J libraries?
  • Can I combine gene expression data from 3' and 5' assay chemistries?
  • How to create a Cell Ranger compatible V(D)J reference?
  • What are productive contigs?
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