diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index de075fcc3224dbaeec9cddb339e5d16fd7d50cdc..97662488912f0f972f511ffedcd95097373f09cc 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -1011,9 +1011,10 @@ rule merge_bigwig_reps:
 
 
 rule join_all_counts:
-    """concat counts for base biotypes into all"""
+    """concat counts for all biotypes into all"""
     input:
-        counts_tables = expand(OPJ(output_dir, "{{trimmer}}", aligner, "mapped_C_elegans", "{{counter}}", "all_on_C_elegans", "{biotype}_{{orientation}}_counts.txt"), biotype=[bty for bty in COUNT_BIOTYPES if bty[-9:] != "_families"]),
+        #counts_tables = expand(OPJ(output_dir, "{{trimmer}}", aligner, "mapped_C_elegans", "{{counter}}", "all_on_C_elegans", "{biotype}_{{orientation}}_counts.txt"), biotype=[bty for bty in COUNT_BIOTYPES if bty[-9:] != "_families"]),
+        counts_tables = expand(OPJ(output_dir, "{{trimmer}}", aligner, "mapped_C_elegans", "{{counter}}", "all_on_C_elegans", "{biotype}_{{orientation}}_counts.txt"), biotype=COUNT_BIOTYPES),
     output:
         counts_table = OPJ(output_dir, "{trimmer}", aligner, "mapped_C_elegans", "{counter}", "all_on_C_elegans", "alltypes_{orientation}_counts.txt"),
     run:
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index d79a509f992ecb2e955254e21928694e346d164c..2cf6a1a80dbdb87f5ce0dcde9acb75a13ed7b293 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -34,6 +34,9 @@ def formatwarning(message, category, filename, lineno, line):
 warnings.formatwarning = formatwarning
 
 import numpy as np
+import matplotlib as mpl
+# To be able to run the script without a defined $DISPLAY
+mpl.use("PDF")
 import pandas as pd
 # To catch errors when plotting KDE
 from scipy.linalg import LinAlgError
@@ -733,9 +736,10 @@ rule merge_bigwig_reps:
 
 
 rule join_all_counts:
-    """concat counts for base biotypes into all"""
+    """concat counts for all biotypes into all"""
     input:
-        counts_tables = expand(OPJ(mapping_dir, aligner, "mapped_C_elegans", "{{counter}}", "all_on_C_elegans", "{biotype}_{{orientation}}_counts.txt"), biotype=[bty for bty in BIOTYPES if bty[-9:] != "_families"]),
+        #counts_tables = expand(OPJ(mapping_dir, aligner, "mapped_C_elegans", "{{counter}}", "all_on_C_elegans", "{biotype}_{{orientation}}_counts.txt"), biotype=[bty for bty in BIOTYPES if bty[-9:] != "_families"]),
+        counts_tables = expand(OPJ(mapping_dir, aligner, "mapped_C_elegans", "{{counter}}", "all_on_C_elegans", "{biotype}_{{orientation}}_counts.txt"), biotype=BIOTYPES),
     output:
         counts_table = OPJ(mapping_dir, aligner, "mapped_C_elegans", "{counter}", "all_on_C_elegans", "alltypes_{orientation}_counts.txt"),
     run: