Software
- 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?
- Will the V(D)J pipeline work without a reference?
- Why is the same TRB chain paired with TRA in clonotype1 and alone in clonotype2?
- Why is the D gene annotation missing in several TCR beta chains?
- 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 detect 2 different alpha chains in the same cell?
- Can we tell which barcodes contain multiple cells 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?
- Why are more reads expressed/mapped for TRB than TRA?
- How are full length TCR/Ig contigs assembled for a Single Cell V(D)J library?