How do I identify cells containing a Transgene in my 10x Chromium scRNAseq data

Question

[Noora]

I am working on a 3’ library 10x genomic data set. I have completed QC, normalization, integration, and annotation with Seurat.

Within the cells in this data set, there are T-cells that express GFP. Would it be possible to identify those cells. Is there anyway to input the GFP sequence and align the data to it as a reference? How would I go about doing this?

Answer 1

[ATpoint]

You will need to include the GFP to the reference and then quantify against that. Posthoc analysis will be difficult, much easier to simply rerun the preprocessing. What did you use? CellRanger?

Technically, for CellRanger, you would need to add the GFP cDNA sequence to both the genome and the GTF and then make a new index, then run CR on that. For other solutions such as Alevin you would need to add the cDNA to the transcriptome fasta file.