diff --git a/R/integration.R b/R/integration.R
index d504f41..9d3a2cd 100644
--- a/R/integration.R
+++ b/R/integration.R
@@ -62,11 +62,15 @@ integrate_assays <- function(mapped,
     #-------------------------------------------------------------------------#
     query_map <- check_maps(mapped)
     query_counts <- get_counts(mapped, type = use_counts)
-    from <- query_map$from
+    from <- sub("-.*", "", query_map$from)
     query_counts <- query_counts[, match(from, colnames(query_counts))]
+    colnames(query_counts) <- make.unique(colnames(query_counts), sep = "-")
     reference_counts <- get_counts(reference, type = use_counts)
-    to <- query_map$to
-    reference_counts <- reference_counts[, match(to, colnames(reference_counts))] 
+    to <- sub("-.*", "", query_map$to)
+    reference_counts <- reference_counts[,
+        match(to, colnames(reference_counts))] 
+    colnames(reference_counts) <- make.unique(
+        colnames(reference_counts), sep = "-")
     #-------------------------------------------------------------------------#
     # Count integration using Seurat methods 
     #-------------------------------------------------------------------------#
diff --git a/R/misc.R b/R/misc.R
index dc9c684..67a6e01 100644
--- a/R/misc.R
+++ b/R/misc.R
@@ -56,7 +56,7 @@ listify <- function(mat) {
 
 remove_suffix <- function(barcodes) {
     prefix <- sapply(barcodes, function(dat){
-        prefix <- paste0(strsplit(x = dat, split = "-")[[1]][1:2], collapse = "-")
+        prefix <- paste0(strsplit(x = dat, split = "*")[[1]][1:2], collapse = "*")
         return(prefix)
     })
     return(prefix)