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I am very new to single cell rna seq analysis, I used to biomaRt to get my gene names using this code

annot<-getBM(c("ensembl_gene_id", "chromosome_name","ensembl_transcript_id", "strand", "start_position", "end_position","gene_biotype","mgi_symbol"),values = cafs, mart=ensemblmart102)

where cafs is the data that I have downloaded in the form of csv.

then I was trying to get top10 genes in my data using

 cafs.object <- FindVariableFeatures(cafs.object, selection.method = "vst", nfeatures = 2000)

top10 <- head(VariableFeatures(cafs.object), 10)

but what I got

[1] "13208" "5685"  "2699"  "3184"  "2700"  "7137"

and I was wondering if there is something wrong that I am doing

Andre Wildberg
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Maryam
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  • You should rename features in the object from HGNC to gene names. https://github.com/satijalab/seurat/issues/2617 – Hixon Jan 12 '23 at 21:31

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