Software
- 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 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?
- What determines which alpha chain gets matched to which beta chain for a particular cell barcode?
- Where can I find isotype information for V(D)J libraries?
- Can IgA1 and IgA2 be detected 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 we pick up SNPs and other mutations in 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?
- Will the V(D)J pipeline work without a reference?
- What genes and criteria were used for clustering the lung cancer data in the 5' GEX and V(D)J integrated tutorial?
- 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 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 to TRB than TRA?
- How are full length TCR/Ig contigs assembled for a Single Cell V(D)J library?