Issues with custom annotation

[kryptonitecircuit2002]

Discussed in #1848

^{Originally posted by kryptonitecircuit2002 November 25, 2024}
Hello everyone!

I am analyzing 10X single cell gene expression and ATAC multiome data for the first time. I am trying to make custom annotation for Zebrafish genome. However I have been facing a lot of issues. This is the pipeline I used following Signac vignette:

hub <- AnnotationHub()
query(hub, "Danio rerio")
ensdb <- hub[["AH116259"]] 
annotations <- GetGRangesFromEnsDb(ensdb = ensdb)
seqlevelsStyle(annotations) <- 'UCSC'
genome(annotations) <- "GRCz11"
grange.counts <- StringToGRanges(rownames(atac_counts), sep = c(":", "-"))
grange.use <- seqnames(grange.counts) %in% standardChromosomes(grange.counts)
atac_counts <- atac_counts[as.vector(grange.use), ]

And this is the latest issue that I am facing:

CoveragePlot(Control.data, region = "mitfa", features = 'mitfa', assay = 'ATAC', expression.assay = 'SCT', peaks = TRUE)
Error in colnames<-(*tmp*, value = start(x = region):end(x = region)) : 
  attempt to set 'colnames' on an object with less than two dimensions
  

Can anyone please help me sort out the issue?

[timoast]

It's possible this could be happening if there are zero counts in the region. Can you check if there are fragments present within the region you're plotting? Can you also show the output of sessionInfo()?