Fail to annotate chromosome data to single cell sequencing data obtained from cellranger
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yw24418 • 0
Last seen 1 day ago
United Kingdom

Hi, I have exactly the same problem mentioned in this post: fail to annotate chromosome data to single cell object When annotating my single cell data obtained from cellranger (with their latest human (GRCh38) reference) using AnnotationHub, some of my genes (about 200) cannot be annotated. I tried to use different versions of EnsDb but this does not help. My codes are here:

ah <- AnnotationHub()
ens.hs.107<- query(ah, c("Homo sapiens", "EnsDb", 107))[[1]] 
genes <- rowData(sce)$ID #sce is my single cell object 
gene_annot <- AnnotationDbi::select(ens.hs.107, 
                                    keys = genes,
                                    keytype = "GENEID",
                                    columns = c("GENEID", "SEQNAME")) %>% set_names(c("ID", "Chromosome"))

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

Error in .local(x, ..., value = value) : 
  34085 rows in value to replace 34202rows
AnnotationHubSoftware SingleCellData annotationTools • 143 views
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Does this include anything you could not get from the GTF that ships with CellRanger? GeneID and chromosome is part of the GTF, so simply load it via rtracklayer::import and filter for what you need.

Entering edit mode
Last seen 1 day ago
United States

The file from 10x is dated 2020, which means it is build 99-101. What I usually do when trying to identify an Ensembl build is to take the gene IDs that don't match the reference and search for that version on Most have probably been removed, and it will tell you in which version that happened.

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