diff --git a/Degradome-seq/Degradome-seq.snakefile b/Degradome-seq/Degradome-seq.snakefile
index 16285272ec21e65bd02ce81e9b1cb35e9a58bf22..ccd8c3859f4c6a8edf021dafce767d05516bdd73 100644
--- a/Degradome-seq/Degradome-seq.snakefile
+++ b/Degradome-seq/Degradome-seq.snakefile
@@ -362,7 +362,7 @@ rule join_all_counts:
             counts_dir,
             f"all_on_{genome}", "alltypes_{orientation}_counts.txt"),
     run:
-        counts_data = pd.concat((pd.read_table(table, index_col="gene") for table in input.counts_tables)).drop_duplicates()
+        counts_data = pd.concat((pd.read_table(table, index_col="gene") for table in input.counts_tables))
         assert len(counts_data.index.unique()) == len(counts_data.index), "Some genes appear several times in the counts table."
         counts_data.index.names = ["gene"]
         counts_data.to_csv(output.counts_table, sep="\t")
diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index 7e1882b08903bab45e586ffcf94ef46ced85047d..f7dca2829dfd2babbb7475af445116aa92d96cf1 100644
--- a/PRO-seq/PRO-seq.snakefile
+++ b/PRO-seq/PRO-seq.snakefile
@@ -932,7 +932,7 @@ rule join_all_counts:
     wildcard_constraints:
         biotype = "|".join(JOINED_BIOTYPES)
     run:
-        counts_data = pd.concat((pd.read_table(table, index_col="gene") for table in input.counts_tables)).drop_duplicates()
+        counts_data = pd.concat((pd.read_table(table, index_col="gene") for table in input.counts_tables))
         assert len(counts_data.index.unique()) == len(counts_data.index), "Some genes appear several times in the counts table."
         counts_data.index.names = ["gene"]
         counts_data.to_csv(output.counts_table, sep="\t")
diff --git a/RNA_Seq_Cecere/RNA-seq.snakefile b/RNA_Seq_Cecere/RNA-seq.snakefile
index 348b940ffaa270ea6d0cf08ba4c87ce7eabd0474..fd2c89c7d62c87500b7ac6c0d9a11cf3f09e8eac 100644
--- a/RNA_Seq_Cecere/RNA-seq.snakefile
+++ b/RNA_Seq_Cecere/RNA-seq.snakefile
@@ -1539,7 +1539,7 @@ rule join_all_counts:
     wildcard_constraints:
         biotype = "|".join(JOINED_BIOTYPES)
     run:
-        counts_data = pd.concat((pd.read_table(table, index_col="gene") for table in input.counts_tables)).drop_duplicates()
+        counts_data = pd.concat((pd.read_table(table, index_col="gene") for table in input.counts_tables))
         assert len(counts_data.index.unique()) == len(counts_data.index), "Some genes appear several times in the counts table."
         counts_data.index.names = ["gene"]
         counts_data.to_csv(output.counts_table, sep="\t")
diff --git a/Ribo-seq/Ribo-seq.snakefile b/Ribo-seq/Ribo-seq.snakefile
index b33d2ebbe0c352bc01703ecc090849fb25da0cdb..fe5a3e094bea4c7905e3f1a4b085bce07d94ba39 100644
--- a/Ribo-seq/Ribo-seq.snakefile
+++ b/Ribo-seq/Ribo-seq.snakefile
@@ -674,7 +674,7 @@ rule trim:
         nb_trimmed =  OPJ(data_dir, "trimmed", "{lib}_{rep}_nb_trimmed.txt"),
     #threads: 2
     message:
-        "Trimming adaptor from raw data, deduplicating reads, removing random 5' {trim5}-mers and 3' {trim3}-mers for {wildcards.lib}_{wildcards.rep}."
+        "Trimming adaptor from raw data, removing random 5' {trim5}-mers and 3' {trim3}-mers for {wildcards.lib}_{wildcards.rep}."
     benchmark:
         OPJ(log_dir, "trim", "{lib}_{rep}_benchmark.txt")
     log:
@@ -1253,7 +1253,10 @@ rule join_all_counts:
         counts_table = OPJ(counts_dir,
         "all_{read_type}_on_%s" % genome, "alltypes_{orientation}_counts.txt"),
     run:
-        counts_data = pd.concat((pd.read_table(table, index_col="gene") for table in input.counts_tables)).drop_duplicates()
+        # !! drop_duplicates() is wrong: doesn't consider the index (at least in pandas < 1.0.0),
+        # so it eliminates rows having the same data pattern. For instance [0, 0, ...] (wich eliminates a lot of entries)
+        # counts_data = pd.concat((pd.read_table(table, index_col="gene") for table in input.counts_tables)).drop_duplicates()
+        counts_data = pd.concat((pd.read_table(table, index_col="gene") for table in input.counts_tables))
         assert len(counts_data.index.unique()) == len(counts_data.index), "Some genes appear several times in the counts table."
         counts_data.index.names = ["gene"]
         counts_data.to_csv(output.counts_table, sep="\t")
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index bd71de78518db09e5aea7b390b0c0f7d4881f30c..d2a5ee467beee94c0d71db1fd4d556b5e35ebd8a 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/small_RNA-seq/small_RNA-seq.snakefile
@@ -1279,7 +1279,7 @@ rule join_all_feature_counts:
         ## debug:
         print("Input:", ", ".join(input))
         ##
-        counts_data = pd.concat((pd.read_table(table, index_col="gene") for table in input.counts_tables)).drop_duplicates()
+        counts_data = pd.concat((pd.read_table(table, index_col="gene") for table in input.counts_tables))
         assert len(counts_data.index.unique()) == len(counts_data.index), "Some genes appear several times in the counts table."
         counts_data.index.names = ["gene"]
         counts_data.to_csv(output.counts_table, sep="\t")