Genes in 10x don't match genes in ENSBL
0
0
Entering edit mode
16 months ago
Sandra ▴ 10

Hi everyone,

I am trying to map my genes to chromosome location so I can remove low-quality cells using high mitochondrial content. When mapping to the chromosomes I obtain the below error.

ah = AnnotationHub()

gene_annot <- AnnotationDbi::select(ens.hs.101, keys = genes, keytype = "GENEID", columns = c("GENEID", "SEQNAME")) %>% set_names(c("ID", "Chromosome"))

genes <- rowData(sce)$ID

rowData(sce) <- merge(rowData(sce), gene_annot, by = "ID", sort=FALSE)

Error in .local(x, ..., value = value) : 26634 rows in value to replace 26664rows

I am thinking there is an error on the gene ID

gene_mapping bioconductor singleCellRNAseq • 1.2k views
ADD COMMENT
1
Entering edit mode

you don't need to determine the chromosome - the best approach is to know what the mt genes are named. I believe the human mt genes will start with MT in the gene symbol. See this example from Seurat:

pbmc[["percent.mt"]] <- PercentageFeatureSet(pbmc, pattern = "^MT-")
ADD REPLY
0
Entering edit mode

I am using Bioconductor packages for analysis and am not familiar with Seurat. I was thinking that the difference in gene IDs might have been eliminated during the cellRanger pipeline.?

ADD REPLY
1
Entering edit mode

If you used cellranger to process the sequencing data then use the gene ids provided by cellranger. Whether you use Bioconductor packages or not doesn't matter.

If you want mitochondrial genes then pull the gene ids for mitochondrial genes based on the "MT-" designation in the gene symbol.

e.g.,

mt_genes <- grep("^MT-", rownames(sce))
ADD REPLY
0
Entering edit mode

Do not mix and match annotations. If you are using 10x provided indexes/annotations when you did cellranger pipeline then stay with that set.

ADD REPLY
0
Entering edit mode

I am trying to add chromosome ids to my rowData based on the gene id

ADD REPLY
0
Entering edit mode

10x may have used an older/newer release of Ensembl (check on that by looking at the metadata/release notes). That may explain the difference you are observing.

ADD REPLY

Login before adding your answer.

Traffic: 2727 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6