10X Genomics Cellranger Transcriptome Alignment for Homo Sapiens and Epstein-Barr virus (EBV) Simuetaneously

Question

[Wu-Sheng Zhang]

I am trying to process scRNA-seq data (10X) from a Homo Sapiens cancer cell line. I have a set of processed files including filtered matrix in .h5 and others processed by cellranger. However, my collaborators also want me to align some EBV genes, e.g., EBNA2, LMP1, etc., so that we could further perform differential analysis.

The ideal case is that I customize some places in the cellranger pipeline, and finally I would have a new filtered h5 matrix with both of Homo Sapiens genes and EBV genes, and then I would not change my downstream analysis script. But I do not have any idea about this. May I have your suggestions? Thank you very much.

Answer 1

[Dave Carlson]

If you have the EBV genome fasta file and annotation GTF file, you can combine them with the human reference data and create a custom reference for use with CellRanger. 10X has instructions on how to do this here.