Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
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25 days ago
ev97 ▴ 20

I have encountered a public dataset which has a genes.tsv file per sample that contains 2 columns: gene_id and gene_name.

I know that the command Seurat::Read10X allows you to decide which column you want to use (gene id or gene names). By default, it will take the second column.

Read10X(
  data.dir,
  gene.column = 2,
  cell.column = 1,
  unique.features = TRUE,
  strip.suffix = FALSE
)

Here a post about this: https://github.com/satijalab/seurat/issues/630

However, what if you want to keep both? Is it possible to have the IDs or the gene name as a layer in the seurat object and not losing it?

I would like to work with Ensembl IDs but use the gene names for plotting, for example.

Does anybody know if this is possible?

Thanks in advance

Seurat single-cell scRNA-seq • 124 views
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