diff --git a/DESCRIPTION b/DESCRIPTION
index b4aa4e6..76a72bb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: wilson
 Type: Package
 Title: Web-Based Interactive Omics Visualization
-Version: 2.1.0
+Version: 2.1.1
 Authors@R: c(
     person("Hendrik", "Schultheis", email = "hendrik.schultheis@mpi-bn.mpg.de", role = c("aut", "cre")),
     person("Jens", "Preussner", email = "jens.preussner@mpi-bn.mpg.de", role = "aut"),
diff --git a/NEWS.md b/NEWS.md
index b73fa15..4b8d2f4 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,5 @@
+# wilson 2.1.1
+- fixed multiple unique_id bug in tobias_parser
 # wilson 2.1.0
 - implemented tobias_parser
 # wilson 2.0.3
diff --git a/R/clarion.R b/R/clarion.R
index 15e3e1a..3c6e1e3 100644
--- a/R/clarion.R
+++ b/R/clarion.R
@@ -56,7 +56,7 @@ Clarion <- R6::R6Class("Clarion",
                            # return unique_id
                            # if no type return first feature
                            if (is.element("type", names(self$metadata))) {
-                             return(self$metadata[type == "unique_id"][["key"]])
+                             return(self$metadata[type == "unique_id"][["key"]][1])
                            } else {
                              return(self$metadata[level == "feature"][["key"]][1])
                            }
@@ -201,6 +201,10 @@ Clarion <- R6::R6Class("Clarion",
                              if (!is.element("unique_id", self$metadata[["type"]])) {
                                stop("Metadata: No unique_id defined in type! Please define a unique_id.")
                              }
+                             # case: multiple unique_ids
+                             if (sum(is.element(self$metadata[["type"]], "unique_id")) > 1) {
+                               warning("Metadata: Found multiple unique_ids! Only first will be used.")
+                             }
                              # case: type = array but no delimiter
                              if (is.element("array", self$metadata[["type"]]) && !is.element("delimiter", names(self$header))) {
                                stop("Found type=array but no delimiter! Columns with multi-value fields require delimiter (in header) and type=array (in metadata).")
diff --git a/R/parser.R b/R/parser.R
index 9e38855..c2ca756 100644
--- a/R/parser.R
+++ b/R/parser.R
@@ -393,14 +393,14 @@ parser <- function(file, dec = ".") {
 #' @param condition_pattern Used to identify condition names by matching und removing given pattern with \code{\link[base]{grep}}. Ignored when condition_names is set.
 #' @param in_field_delimiter Delimiter for multi value fields. Default = ','.
 #' @param dec Decimal separator. Used in file reading and writing.
-#' @param unique_id Whether the table contains an unique id column. If FALSE (default) will create one at first position.
 #' @param ... Used as header information.
 #'
 #' @details During conversion the parser will try to use the given config (if provided) to create the \href{https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format}{Clarion} metadata. In the case of insufficient config information it will try to approximate by referencing condition names issuing warnings in the process.
+#' @details As the format requires an unqiue id the parser will create one if necessary.
 #' @details Factor grouping (metadata factor columns) is currently not implemented!
 #'
 #' @export
-tobias_parser <- function(input, output, filter_columns = NULL, filter_pattern = NULL, config = system.file("extdata", "tobias_config.json", package = "wilson"), omit_NA = FALSE, condition_names = NULL, condition_pattern = "_bound$", in_field_delimiter = ",", dec = ".", unique_id = FALSE, ...) {
+tobias_parser <- function(input, output, filter_columns = NULL, filter_pattern = NULL, config = system.file("extdata", "tobias_config.json", package = "wilson"), omit_NA = FALSE, condition_names = NULL, condition_pattern = "_bound$", in_field_delimiter = ",", dec = ".", ...) {
   ## filter data columns
   # check if filter columns is a file or a vector
   if (!is.null(filter_columns) && file.exists(filter_columns)) {
@@ -432,14 +432,6 @@ tobias_parser <- function(input, output, filter_columns = NULL, filter_pattern =
     data <- stats::na.omit(data)
   }
 
-  # create id column
-  if (!unique_id) {
-    data[, "id" := seq_len(nrow(data))]
-    # move id column to first position
-    new_order <- c("id", names(data)[ names(data) != "id"])
-    data <- data[, new_order, with = FALSE]
-  }
-
   ##### metadata
   metadata <- data.table::data.table(names(data))
 
@@ -558,7 +550,22 @@ tobias_parser <- function(input, output, filter_columns = NULL, filter_pattern =
 
   # set unique_id fallback
   if (!any(metadata[["type"]] == "unique_id")) {
-    metadata[key == unique_id_fallback, "type"] <- "unique_id"
+    if (!is.null(unique_id_fallback)) {
+      metadata[key == unique_id_fallback, "type"] <- "unique_id"
+    } else {
+      # setup unique_id column if there is neither a defined column nor a fallback
+
+      # create id column
+      data[, "id" := seq_len(nrow(data))]
+      # move id column to first position
+      new_order <- c("id", names(data)[ names(data) != "id"])
+      data <- data[, new_order, with = FALSE]
+
+      id_row <- data.table::data.table("id", level = "feature", type = "unique_id", label = "id", sub_label = "")
+      names(id_row)[1] <- "key"
+      # add meta entry
+      metadata <- rbind(id_row, metadata)
+    }
   }
 
   ##### header
diff --git a/inst/extdata/tobias_config.json b/inst/extdata/tobias_config.json
index f8e050a..9a2c5dc 100644
--- a/inst/extdata/tobias_config.json
+++ b/inst/extdata/tobias_config.json
@@ -1,12 +1,5 @@
 {
   "meta": [
-    {
-      "col_name": "id",
-      "level": "feature",
-      "type": "unique_id",
-      "label": "id",
-      "sublabel": ""
-    },
     {
       "col_name": "TFBS_chr",
       "level": "feature",
@@ -140,146 +133,6 @@
       "label": "name",
       "sublabel": "gene"
     },
-    {
-      "col_name": "2C_score",
-      "level": "condition",
-      "type": "score",
-      "label": "2C",
-      "sublabel": "score"
-    },
-    {
-      "col_name": "8C_score",
-      "level": "condition",
-      "type": "score",
-      "label": "8C",
-      "sublabel": "score"
-    },
-    {
-      "col_name": "ICM_score",
-      "level": "condition",
-      "type": "score",
-      "label": "ICM",
-      "sublabel": "score"
-    },
-    {
-      "col_name": "naive_hESC_score",
-      "level": "condition",
-      "type": "score",
-      "label": "naive hESC",
-      "sublabel": "score"
-    },
-    {
-      "col_name": "hESC_score",
-      "level": "condition",
-      "type": "score",
-      "label": "hESC",
-      "sublabel": "score"
-    },
-    {
-      "col_name": "2C_bound",
-      "level": "condition",
-      "type": "score",
-      "label": "2C",
-      "sublabel": "bound"
-    },
-    {
-      "col_name": "8C_bound",
-      "level": "condition",
-      "type": "score",
-      "label": "8C",
-      "sublabel": "bound"
-    },
-    {
-      "col_name": "ICM_bound",
-      "level": "condition",
-      "type": "score",
-      "label": "ICM",
-      "sublabel": "bound"
-    },
-    {
-      "col_name": "naive_hESC_bound",
-      "level": "condition",
-      "type": "score",
-      "label": "naive hESC",
-      "sublabel": "bound"
-    },
-    {
-      "col_name": "hESC_bound",
-      "level": "condition",
-      "type": "score",
-      "label": "hESC",
-      "sublabel": "bound"
-    },
-    {
-      "col_name": "2C_8C_log2fc",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "2C|8C",
-      "sublabel": "log2fc"
-    },
-    {
-      "col_name": "2C_ICM_log2fc",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "2C|ICM",
-      "sublabel": "log2fc"
-    },
-    {
-      "col_name": "2C_naive_hESC_log2fc",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "2C|naive hESC",
-      "sublabel": "log2fc"
-    },
-    {
-      "col_name": "2C_hESC_log2fc",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "2C|hESC",
-      "sublabel": "log2fc"
-    },
-    {
-      "col_name": "8C_ICM_log2fc",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "8C|ICM",
-      "sublabel": "log2fc"
-    },
-    {
-      "col_name": "8C_naive_hESC_log2fc",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "8C|naive hESC",
-      "sublabel": "log2fc"
-    },
-    {
-      "col_name": "8C_hESC_log2fc",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "8C|hESC",
-      "sublabel": "log2fc"
-    },
-    {
-      "col_name": "ICM_naive_hESC_log2fc",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "ICM|naive hESC",
-      "sublabel": "log2fc"
-    },
-    {
-      "col_name": "ICM_hESC_log2fc",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "ICM|hESC",
-      "sublabel": "log2fc"
-    },
-    {
-      "col_name": "naive_hESC_hESC_log2fc",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "naive hESC|hESC",
-      "sublabel": "log2fc"
-    },
     // overview columns
     {
       "col_name": "TF_name",
@@ -301,216 +154,6 @@
       "type": "category",
       "label": "total TFBS",
       "sublabel": ""
-    },
-    {
-      "col_name": "2C_mean_score",
-      "level": "condition",
-      "type": "score",
-      "label": "2C",
-      "sublabel": "mean"
-    },
-    {
-      "col_name": "2C_bound",
-      "level": "condition",
-      "type": "score",
-      "label": "2C",
-      "sublabel": "bound"
-    },
-    {
-      "col_name": "8C_mean_score",
-      "level": "condition",
-      "type": "score",
-      "label": "8C",
-      "sublabel": "mean"
-    },
-    {
-      "col_name": "8C_bound",
-      "level": "condition",
-      "type": "score",
-      "label": "8C",
-      "sublabel": "bound"
-    },
-    {
-      "col_name": "ICM_mean_score",
-      "level": "condition",
-      "type": "score",
-      "label": "ICM",
-      "sublabel": "mean"
-    },
-    {
-      "col_name": "ICM_bound",
-      "level": "condition",
-      "type": "score",
-      "label": "ICM",
-      "sublabel": "bound"
-    },
-    {
-      "col_name": "naive_hESC_mean_score",
-      "level": "condition",
-      "type": "score",
-      "label": "naive_hESC",
-      "sublabel": "mean"
-    },
-    {
-      "col_name": "naive_hESC_bound",
-      "level": "condition",
-      "type": "score",
-      "label": "naive_hESC",
-      "sublabel": "bound"
-    },
-    {
-      "col_name": "hESC_mean_score",
-      "level": "condition",
-      "type": "score",
-      "label": "hESC",
-      "sublabel": "mean"
-    },
-    {
-      "col_name": "hESC_bound",
-      "level": "condition",
-      "type": "score",
-      "label": "hESC",
-      "sublabel": "bound"
-    },
-    {
-      "col_name": "2C_8C_change",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "2C|8C",
-      "sublabel": "change"
-    },
-    {
-      "col_name": "2C_8C_pvalue",
-      "level": "contrast",
-      "type": "probability",
-      "label": "2C|8C",
-      "sublabel": "p-value"
-    },
-    {
-      "col_name": "2C_ICM_change",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "2C|ICM",
-      "sublabel": "change"
-    },
-    {
-      "col_name": "2C_ICM_pvalue",
-      "level": "contrast",
-      "type": "probability",
-      "label": "2C|ICM",
-      "sublabel": "p-value"
-    },
-    {
-      "col_name": "2C_naive_hESC_change",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "2C|naive hESC",
-      "sublabel": "change"
-    },
-    {
-      "col_name": "2C_naive_hESC_pvalue",
-      "level": "contrast",
-      "type": "probability",
-      "label": "2C|naive hESC",
-      "sublabel": "p-value"
-    },
-    {
-      "col_name": "2C_hESC_change",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "2C|hESC",
-      "sublabel": "change"
-    },
-    {
-      "col_name": "2C_hESC_pvalue",
-      "level": "contrast",
-      "type": "probability",
-      "label": "2C|hESC",
-      "sublabel": "p-value"
-    },
-    {
-      "col_name": "8C_ICM_change",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "8C|ICM",
-      "sublabel": "change"
-    },
-    {
-      "col_name": "8C_ICM_pvalue",
-      "level": "contrast",
-      "type": "probability",
-      "label": "8C|ICM",
-      "sublabel": "p-value"
-    },
-    {
-      "col_name": "8C_naive_hESC_change",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "8C|naive hESC",
-      "sublabel": "change"
-    },
-    {
-      "col_name": "8C_naive_hESC_pvalue",
-      "level": "contrast",
-      "type": "probability",
-      "label": "8C|naive hESC",
-      "sublabel": "p-value"
-    },
-    {
-      "col_name": "8C_hESC_change",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "8C|hESC",
-      "sublabel": "change"
-    },
-    {
-      "col_name": "8C_hESC_pvalue",
-      "level": "contrast",
-      "type": "probability",
-      "label": "8C|hESC",
-      "sublabel": "p-value"
-    },
-    {
-      "col_name": "ICM_naive_hESC_change",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "ICM|naive hESC",
-      "sublabel": "change"
-    },
-    {
-      "col_name": "ICM_naive_hESC_pvalue",
-      "level": "contrast",
-      "type": "probability",
-      "label": "ICM|naive hESC",
-      "sublabel": "p-value"
-    },
-    {
-      "col_name": "ICM_hESC_change",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "ICM|hESC",
-      "sublabel": "change"
-    },
-    {
-      "col_name": "ICM_hESC_pvalue",
-      "level": "contrast",
-      "type": "probability",
-      "label": "ICM|hESC",
-      "sublabel": "p-value"
-    },
-    {
-      "col_name": "naive_hESC_hESC_change",
-      "level": "contrast",
-      "type": "ratio",
-      "label": "naive hESC|hESC",
-      "sublabel": "p-value"
-    },
-    {
-      "col_name": "naive_hESC_hESC_pvalue",
-      "level": "contrast",
-      "type": "probability",
-      "label": "naive hESC|hESC",
-      "sublabel": "change"
     }
   ]
 }
\ No newline at end of file
diff --git a/man/tobias_parser.Rd b/man/tobias_parser.Rd
index c7cafdc..66ce2d6 100644
--- a/man/tobias_parser.Rd
+++ b/man/tobias_parser.Rd
@@ -8,7 +8,7 @@ tobias_parser(input, output, filter_columns = NULL,
   filter_pattern = NULL, config = system.file("extdata",
   "tobias_config.json", package = "wilson"), omit_NA = FALSE,
   condition_names = NULL, condition_pattern = "_bound$",
-  in_field_delimiter = ",", dec = ".", unique_id = FALSE, ...)
+  in_field_delimiter = ",", dec = ".", ...)
 }
 \arguments{
 \item{input}{Path to input table}
@@ -31,8 +31,6 @@ tobias_parser(input, output, filter_columns = NULL,
 
 \item{dec}{Decimal separator. Used in file reading and writing.}
 
-\item{unique_id}{Whether the table contains an unique id column. If FALSE (default) will create one at first position.}
-
 \item{...}{Used as header information.}
 }
 \description{
@@ -41,5 +39,7 @@ Click \href{https://github.molgen.mpg.de/loosolab/TOBIAS}{here} for more informa
 \details{
 During conversion the parser will try to use the given config (if provided) to create the \href{https://github.molgen.mpg.de/loosolab/wilson-apps/wiki/CLARION-Format}{Clarion} metadata. In the case of insufficient config information it will try to approximate by referencing condition names issuing warnings in the process.
 
+As the format requires an unqiue id the parser will create one if necessary.
+
 Factor grouping (metadata factor columns) is currently not implemented!
 }