scRNAseq output generated using STARsolo has gene_id rather than gene_name

Question

[Lauren]

Hello! I am brand new to the world of single-cell RNA seq and all of the software that comes along with it so apologies if this is a basic question. I have been working with a data set from a recently published paper and trying to recreate the data analysis in order to create a guide/pipeline for my lab to use for our own scRNAseq experiments. I finally managed to get the sparse matrix and import it to Seurat for further analysis but upon searching for mitochindrial DNA and rRNA for cell filtering discovered that in my output file the features are all gene id's rather than gene names. I know I could probably find another way around this without reanalyzing the data but I'm a bit confused as to why the gene name is not what was output. Any ideas as to what might have happened or how I could fix it? Thanks!

Answer 1

[dsull]

How are you loading it into Seurat? Search for the features.tsv file in one of the STARsolo output subdirectories (might be somewhere like Solo.out/Gene/raw/features.tsv). It should contain the gene ID in the first column and the gene name/symbol in the second column.

If you load it into Seurat using the ReadMtx function, and specify feature.column=2, then you should get what you need.

[Lauren]

Thank you so much!