Integrate CITESeq reads to Seurat object
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3 months ago

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?

scRNAseq CITEseqCount Seurat CITEseq • 408 views
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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?

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3 months ago
lianov ▴ 10

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