diff --git a/environment.yml b/environment.yml
index 235a804..dd33585 100644
--- a/environment.yml
+++ b/environment.yml
@@ -7,7 +7,8 @@ dependencies:
   - snakemake-minimal
   - samtools
   - cutadapt
-  - bowtie2
+  # The package for Bowtie2 2.4.1 creates VN: tag without value in SAM header
+  - bowtie2 =2.3.5.1
   - je-suite
   - igvtools
   - deeptools