diff --git a/config/multiqc_config.yaml b/config/multiqc_config.yaml
index dd16fbf4c304754aa8763fe627a491088c1778bd..9bff2168e7ef655adce75f1fcb63a7487a830567 100644
--- a/config/multiqc_config.yaml
+++ b/config/multiqc_config.yaml
@@ -93,6 +93,9 @@ extra_fn_clean_exts:
     - _sort
     - _sort_dedup_NoBlacklist
     - _sort_dedup
+    - _R1
+    - _R2
+    - _stats
     - type: remove
       pattern: '.sorted'
     - type: regex