Software
- 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?
- Why are there only a few V(D)J dominant clonotypes in my sample?