Cells in the fragment object disappear after integration

[AyeGonzalezMontoro]

Hi! Thanks a lot for the great software and documentation.

I am using Signac/Seurat to analyze scATCseq data, for which I want to integrate several datasets. I have created several Seurat objects, all with the same set of peaks quantified, in an assay called "cluster_peaks". These objects were combined into "Seurat_combined". Both the original Seurat objects and the combined object contain a fragment object within the "cluster_peaks" assay, with the path to the fragment file, and a variable number of cells, depending on the experiment. However, after integration (Integrate embeddings), the resulting Seurat object has 0 cells in all of the fragment objects, making it impossible to run subsequent functions like GeneActivity or CoveragePlot. I paste below this part of the code, and a screen capture of how the objects "Seurat_combined" and "Seurat_integrated" look like.
I am happy to add more information if necessary.

load("./RObjects/Seurat_objects_filtered_Cl1.RData")

Seurat_objects_filtered$BAF200_534$dataset <- 'BAF200_534'
Seurat_objects_filtered$BAF200_WT1$dataset <- 'BAF200_WT1'
Seurat_objects_filtered$BAF200_WT2$dataset <- 'BAF200_WT2'
Seurat_objects_filtered$CHD4_WT_20_L3$dataset <- 'CHD4_WT_20_L3'
Seurat_objects_filtered$CHD4_WT_20_L4$dataset <- 'CHD4_WT_20_L4'
Seurat_objects_filtered$CHD4_WT_480$dataset <- 'CHD4_WT_480'
Seurat_objects_filtered$HP1ag_WT_435$dataset <- 'HP1ag_WT_435'
Seurat_objects_filtered$PBRM1_WT1$dataset <- 'PBRM1_WT1'
Seurat_objects_filtered$PBRM1_WT2$dataset <- 'PBRM1_WT2'


# merge all datasets, adding a cell ID to make sure cell names are unique
Seurat_combined <- merge(
  x = Seurat_objects_filtered$BAF200_534,
  y = list(Seurat_objects_filtered$BAF200_WT1, Seurat_objects_filtered$BAF200_WT2, Seurat_objects_filtered$CHD4_WT_20_L3, Seurat_objects_filtered$CHD4_WT_20_L4, Seurat_objects_filtered$CHD4_WT_480, Seurat_objects_filtered$HP1ag_WT_435, Seurat_objects_filtered$PBRM1_WT1, Seurat_objects_filtered$PBRM1_WT2),
  add.cell.ids = c('BAF200_534', 'BAF200_WT1', 'BAF200_WT2', 'CHD4_WT_20_L3', 'CHD4_WT_20_L4', 'CHD4_WT_480', 'HP1ag_WT_435', 'PBRM1_WT1', 'PBRM1_WT2')
)

Seurat_objects_filtered <- lapply(names(Seurat_objects_filtered), function(obj_name) {
  seurat_obj <- Seurat_objects_filtered[[obj_name]]
  new_barcodes <- paste0(obj_name, "_", colnames(seurat_obj))  # Add prefix to each barcode
  colnames(seurat_obj) <- new_barcodes  # Update cell barcodes
  return(seurat_obj)
})

names(Seurat_objects_filtered) <- c('BAF200_534', 'BAF200_WT1', 'BAF200_WT2', 'CHD4_WT_20_L3', 'CHD4_WT_20_L4', 'CHD4_WT_480', 'HP1ag_WT_435', 'PBRM1_WT1', 'PBRM1_WT2')

integration.anchors <- FindIntegrationAnchors(
  object.list = Seurat_objects_filtered,
  anchor.features = rownames(Seurat_objects_filtered$BAF200_534),
  reduction = "rlsi",
  dims = 2:30
)

Seurat_combined <- RunTFIDF(Seurat_combined)
Seurat_combined <- FindTopFeatures(Seurat_combined, min.cutoff = 20)
Seurat_combined <- RunSVD(Seurat_combined)
Seurat_combined <- RunUMAP(Seurat_combined, reduction = "lsi", dims = 2:30)

# integrate LSI embeddings
Seurat_integrated <-  IntegrateEmbeddings(
  anchorset = integration.anchors,
  reductions = Seurat_combined[["lsi"]],
  new.reduction.name = "integrated_lsi",
  dims.to.integrate = 1:30
)

I would be super grateful for some help on how to solve this issue!

best wishes,

Ayelem