diff --git a/src/RNAseq_sen1D.nf b/src/RNAseq_sen1D.nf
index 3b79021d9820c22173d1352013776b3d0d41d080..fd47a2d4683100c872cf8c786f50ec5c1eea37cc 100644
--- a/src/RNAseq_sen1D.nf
+++ b/src/RNAseq_sen1D.nf
@@ -166,7 +166,7 @@ ${reads[0]} ${reads[1]}
 }
 
 /*
-* Bowtie2 :
+* Bowtie1 :
 * Imputs : fastq files
 * Imputs : fasta files
 * Output : bam files
@@ -195,9 +195,9 @@ process index_fasta {
 
   script:
 """
-bowtie2-build --threads ${task.cpus} ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie2_report.txt
+bowtie-build --threads ${task.cpus} -f ${fasta} ${fasta.baseName}.index &> ${fasta.baseName}_bowtie_report.txt
 
-if grep -q "Error" ${fasta.baseName}_bowtie2_report.txt; then
+if grep -q "Error" ${fasta.baseName}_bowtie_report.txt; then
   exit 1
 fi
 """
@@ -210,7 +210,7 @@ fi
 process mapping_fastq {
   tag "$pair_id"
   cpus 4
-  publishDir "results/mapping/bams/", mode: 'copy'
+  publishDir "results/mapping_bowtie1/bams/", mode: 'copy'
 
   input:
   set pair_id, file(reads) from fastq_files_align
@@ -218,22 +218,24 @@ process mapping_fastq {
 
   output:
   set pair_id, "*.bam" into bam_files
-  file "*_bowtie2_report.txt" into mapping_fastq_report
+  file "*_bowtie1_report.txt" into mapping_fastq_report
 
   script:
   index_id = index[0]
   for (index_file in index) {
-    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/) ) {
-        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+    if (index_file =~ /.*\.1\.ebwt/) {
+        index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
     }
   }
 """
- bowtie2 --very-sensitive -p ${task.cpus} -x ${index_id} \
- -1 ${reads[0]} -2 ${reads[1]} 2> \
- ${pair_id}_bowtie2_report.txt | \
- samtools view -Sb - > ${pair_id}.bam
-
-if grep -q "Error" ${pair_id}_bowtie2_report.txt; then
+# -v specify the max number of missmatch, -k the number of match reported per
+# reads
+bowtie --best -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+-1 ${reads[0]} -2 ${reads[1]} 2> \
+${pair_id}_bowtie_report.txt | \
+samtools view -Sb - > ${pair_id}.bam
+
+if grep -q "Error" ${pair_id}_bowtie_report.txt; then
   exit 1
 fi
 """