Integrate CITESeq reads to Seurat object

Question

[Vinothkumar]

I am trying to integrate my scRNASeq data with a CITESeq matrix. However, my scRNAseq cell barcodes look like XXXXXXXXX-1, whereas the cell barcodes from CITEseq doesn't have the "-1". This causes a problem when trying to integrate the CITEseq sparse matrix into the Seurat object.

In my mind, the solution would be either to remove the "-1" from my Seurat object or to add "-1" to all the cell barcodes in the CITEseq sparse matrix.

But I haven't found a way to do either. What would you suggest?

[Kevin Blighe]

We (my mate Steve and I) looked at CITE-seq data in the past but did not encounter this issue. We followed this tutorial and applied it to or own data: https://satijalab.org/seurat/archive/v3.1/multimodal_vignette.html

Can you explain the data processing steps that have been applied so far, and also the error message(s) received?

Answer 1

[lianov]

When you use Read10X, set strip.suffix = TRUE to the RNA data.