I have 10x scRNA-seq data for a dog. The genes are in ensembl id format. I converted them to gene symbols using biomaRt and added to the Seurat features metadata like this:
HCC1@assays$RNA@meta.features <- merge(HCC1@assays$RNA@meta.features, gfile, by=0, all.x=TRUE)
So my HCC1@assays$RNA@meta.features looks like this
The reason why I do not want to convert features into gene symbols right away is that there are many duplicate gene symbols after conversion. That is why I want to use gene symbols in the end for annotation only.
However, for quality control purposes I need gene names (to find percentages of mitochondrial and ribosomal genes).
Is there a way to refer to the gene names when using PercentageFeatureSet? For example in this line:
HCC1[["percent.rb"]] <- PercentageFeatureSet(HCC1, pattern="^MT-")
•
written
by
fifty_fifty •
1 answer
You can provide the features to use directly via the features parameter of PercentageFeatureSet. So grab whatever gene names match your pattern, get the row name, and feed those in. See ?PercentageFeatureSet for details.
Log in to answer this question.
-
Seurat V5 Subscript Out of Bounds Error
written by KokiBio •
-
Errors with GSEA using clusterProfiler
written by bio_info •
-
QC filtering for 10x Single Cell Gene Expression Flex Fixed RNA Profiling
written by yura.grabovska •
-
batch correction: cds from seurat
written by sooni •
-
Issue with Identifying Mitochondrial Genes in Seurat Analysis with mRatBN7.2 Reference
written by dxj294 •
-
Seurat scRNA convert Ensembl ID to gene symbol
written by clizama •
-
scRNA seq differential gene expression analyses
written by bioinformatics •
-
Non-linear relationship between a cell's mitochondrial content and detection of ribosomal genes sse…
written by charlesgwellem •
-
problem in visualization of Gene names instead of Gene ids in annotated Seurat object
written by Maria17 •
-
Regular Expression For Real World Gene Symbols?
written by Samuel Lampa
