diff --git a/Snakefile b/Snakefile
index 441a403b833eac2758e40d79439c6ee4a91370d0..8f8b8b4cd69e6c791871e6f54f9ecf5af3b375b6 100755
--- a/Snakefile
+++ b/Snakefile
@@ -123,16 +123,19 @@ else:
     adapters_output = input_data
     
 
-#----------------------------------
-# bowtie2 MAPPING on Ribo only
-#----------------------------------
+#-----------------------------------------
+# Estimate ribosomal rate in samples
+#-----------------------------------------
 
    
 if config["genome"]["rRNA_mapping"] :
     sortmerna_input = adapters_output
     sortmerna_fasta = config["genome"]["ribo_fasta_file"]
-    sortmerna_outfile_rRNA = "02-Mapping/Ribo/{SAMPLE}_rRNA.fastq"
-    sortmerna_outfile_no_rRNA = "02-Mapping/Ribo/{SAMPLE}_norRNA.fastq"
+    sortmerna_outfile_rRNA = ["02-Mapping/Ribo/{{SAMPLE}}_rRNA{}.fastq".format(rt1)]
+    sortmerna_outfile_no_rRNA = ["02-Mapping/Ribo/{{SAMPLE}}_norRNA{}.fastq".format(rt1)]
+    if paired:
+        sortmerna_outfile_rRNA += ["02-Mapping/Ribo/{{SAMPLE}}_rRNA{}.fastq".format(rt2)]
+        sortmerna_outfile_no_rRNA += ["02-Mapping/Ribo/{{SAMPLE}}_norRNA{}.fastq".format(rt2)]
     sortmerna_logs_err = "02-Mapping/Ribo/logs/{SAMPLE}_mapping.err"
     sortmerna_logs_out = "02-Mapping/Ribo/logs/{SAMPLE}_mapping.out"
     final_output.extend(expand(sortmerna_outfile_no_rRNA, SAMPLE=samples))
diff --git a/workflow/rules/sortmerna.rules b/workflow/rules/sortmerna.rules
index 6837b05ba3dc79ac1956b7706f2d270ea03dd408..0afde1069bec0bb37701b0fc18809a018af65526 100755
--- a/workflow/rules/sortmerna.rules
+++ b/workflow/rules/sortmerna.rules
@@ -44,17 +44,20 @@ rule sortmerna:
     shell:
         """
         set +o pipefail
+        
         tmp="{input.fastq}"
         infiles=($tmp)
+ 
         fasta="{input.fasta}"
         idxdir=$(dirname ${{fasta}})"/sortmerna/"
-
-
+        
         if [[ ${{#infiles[@]}} -eq 2 ]];
         then
             sortmerna --ref ${{fasta}} --idx-dir ${{idxdir}} --workdir {params.tmpdir} -threads {threads} --reads ${{infiles[0]}} --reads ${{infiles[1]}} --aligned {output.rRNA} --fastx --out2 --paired_out --other {output.no_rRNA}  -v > {log.out} 2> {log.err}
-            mv {output.no_rRNA}.fastq {output.no_rRNA}
-            mv {output.rRNA}.fastq {output.rRNA}
+            mv {output.no_rRNA}_fwd.fastq {output.no_rRNA}[0]
+            mv {output.no_rRNA}_rev.fastq {output.no_rRNA}[1]
+            mv {output.rRNA}_fwd.fastq {output.rRNA}[0]
+            mv {output.rRNA}_rev.fastq {output.rRNA}[1]
 
         else
             sortmerna --ref ${{fasta}} --idx-dir ${{idxdir}} --workdir {params.tmpdir} -threads {threads} --reads ${{infiles[0]}} --aligned {output.rRNA} --fastx --other {output.no_rRNA}  -v > {log.out} 2> {log.err}
diff --git a/workflow/rules/star_mapping_pass1.rules b/workflow/rules/star_mapping_pass1.rules
index 3929b94624a1859e2acda2b8287cdbd935a5182d..b23a131494808d4a2b72377c3a5e13cda4d7788a 100755
--- a/workflow/rules/star_mapping_pass1.rules
+++ b/workflow/rules/star_mapping_pass1.rules
@@ -45,10 +45,8 @@ rule star_mapping_pass1:
         star_mapping_pass1_logs
     shell:
         """ 
-        tmp="{input}"
-        infiles=($tmp)
 
-        if [[ ${{infiles[0]}} == "*.gz"  ]]
+        if [[ {input.fastq[0]} =~ \.gz$ ]]
         then
             STAR --genomeDir {params.index} \
                  --readFilesIn {input.fastq}  \