Error Report: seqinfo error with custom genome in Signac/Seurat

[hayatkhanndsu]

Hello,

I am analyzing single-cell ATAC-seq data using Seurat + Signac with a custom genome reference.
Most steps run correctly, but I encounter an error when accessing the ChromatinAssay from the Seurat object.

library(Signac)
library(Seurat)
library(GenomicRanges)
library(ggplot2)
library(patchwork)

1# Read in data
counts <- Read10X_h5('/Users/hayatkhan/Documents/Hayat/hayat_SZ45_out/filtered_peak_bc_matrix.h5')
counts[1:10,1:10]

chrom_assay <- CreateChromatinAssay(
counts = counts,
sep = c(":", "-"),
fragments = "/Users/hayatkhan/Documents/Hayat/hayat_SZ45_out/fragments.tsv.gz",
min.cells = 10,
min.features = 200)

str(chrom_assay)

metadata <- read.csv(file = '/Users/hayatkhan/Documents/Hayat/hayat_SZ45_out/singlecell.csv',
header = T, row.names = 1)
View(metadata)

---

Error encountered

create a seurat Object

SZ45 <- CreateSeuratObject(counts = chrom_assay, meta.data = metadata, assay = "peaks")

str(SZ45)
SZ45[["peaks"]]
granges(SZ45)

SZ45[["peaks"]]
ChromatinAssay data with 19568 features for 10675 cells
Variable features: 0
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'genome': unable to find an inherited method for function ‘seqinfo’ for signature ‘x = "ChromatinAssay"’

[leecon30]

Try running this and if it works run it at the start of each session.

setMethod(
"seqinfo",
signature(x = "ChromatinAssay"),
function(x) {
GenomeInfoDb::seqinfo(x@ranges)
}
)