diff --git a/code/SoS/data_preprocessing/phenotype/gene_annotation.ipynb b/code/SoS/data_preprocessing/phenotype/gene_annotation.ipynb
index 2de6ed2f3..750b7c06c 100644
--- a/code/SoS/data_preprocessing/phenotype/gene_annotation.ipynb
+++ b/code/SoS/data_preprocessing/phenotype/gene_annotation.ipynb
@@ -63,8 +63,8 @@
     "| `input/rnaseq/protocol_example.leafcutter.intron_count.tsv` | Toy leafcutter intron-count table (IDs `chr:start:end:clu_N_strand`). |\n",
     "| `input/rnaseq/protocol_example.leafcutter.phenotype.bed.gz` | Toy leafcutter intron-excision phenotype matrix. |\n",
     "| `input/rnaseq/protocol_example.psichomics.phenotype.tsv` | Toy psichomics phenotype matrix (IDs end in `_<gene_id>`). |\n",
-    "| `reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.ERCC.gtf` | Collapsed gene-model GTF (gene/protein annotation). |\n",
-    "| `reference_data/Homo_sapiens.GRCh38.103.chr.gtf` | Full gene-model GTF with exons (leafcutter/psichomics). |\n"
+    "| `input/reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.ERCC.gtf` | Collapsed gene-model GTF (gene/protein annotation). |\n",
+    "| `input/reference_data/Homo_sapiens.GRCh38.103.chr.gtf` | Full gene-model GTF with exons (leafcutter/psichomics). |\n"
    ]
   },
   {
@@ -132,7 +132,7 @@
     "sos run pipeline/gene_annotation.ipynb annotate_coord \\\n",
     "    --cwd output/gene_annotation \\\n",
     "    --phenoFile input/rnaseq/protocol_example.rnaseq.bed.gz \\\n",
-    "    --coordinate-annotation reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.ERCC.gtf \\\n",
+    "    --coordinate-annotation input/reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.ERCC.gtf \\\n",
     "    --phenotype-id-column gene_id\n"
    ]
   },
@@ -183,7 +183,7 @@
     "sos run pipeline/gene_annotation.ipynb annotate_coord \\\n",
     "    --cwd output/gene_annotation \\\n",
     "    --phenoFile input/proteomics/protocol_example.protein.no_coord.tsv \\\n",
-    "    --coordinate-annotation reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.ERCC.gtf \\\n",
+    "    --coordinate-annotation input/reference_data/Homo_sapiens.GRCh38.103.chr.reformatted.collapse_only.gene.ERCC.gtf \\\n",
     "    --phenotype-id-column gene_id \\\n",
     "    --molecular-trait-type protein\n"
    ]
@@ -227,7 +227,7 @@
     "    --cwd output/gene_annotation \\\n",
     "    --phenoFile input/rnaseq/protocol_example.leafcutter.phenotype.bed.gz \\\n",
     "    --intron-count input/rnaseq/protocol_example.leafcutter.intron_count.tsv \\\n",
-    "    --coordinate-annotation reference_data/Homo_sapiens.GRCh38.103.chr.gtf \\\n",
+    "    --coordinate-annotation input/reference_data/Homo_sapiens.GRCh38.103.chr.gtf \\\n",
     "    --map-stra site\n"
    ]
   },
@@ -293,7 +293,7 @@
     "    --cwd output/gene_annotation \\\n",
     "    --phenoFile input/rnaseq/protocol_example.leafcutter.phenotype.bed.gz \\\n",
     "    --intron-count input/rnaseq/protocol_example.leafcutter.intron_count.tsv \\\n",
-    "    --coordinate-annotation reference_data/Homo_sapiens.GRCh38.103.chr.gtf \\\n",
+    "    --coordinate-annotation input/reference_data/Homo_sapiens.GRCh38.103.chr.gtf \\\n",
     "    --map-stra site\n"
    ]
   },
@@ -335,7 +335,7 @@
     "sos run pipeline/gene_annotation.ipynb annotate_psichomics_isoforms \\\n",
     "    --cwd output/gene_annotation \\\n",
     "    --phenoFile input/rnaseq/protocol_example.psichomics.phenotype.tsv \\\n",
-    "    --coordinate-annotation reference_data/Homo_sapiens.GRCh38.103.chr.gtf\n"
+    "    --coordinate-annotation input/reference_data/Homo_sapiens.GRCh38.103.chr.gtf\n"
    ]
   },
   {
@@ -622,9 +622,7 @@
    "metadata": {
     "kernel": "SoS"
    },
-   "source": [
-    "The gtf used here should be the collapsed gtf, i.e. the final output of reference_data gtf processing and the one used to called rnaseq."
-   ]
+   "source": "The gtf used here should be the collapsed gtf, i.e. the final output of reference_data gtf processing and the one used to called rnaseq."
   },
   {
    "cell_type": "code",
diff --git a/code/script/molecular_phenotypes/QC/bulk_expression_QC.R b/code/script/molecular_phenotypes/QC/bulk_expression_QC.R
index ea7400526..7fef50261 100644
--- a/code/script/molecular_phenotypes/QC/bulk_expression_QC.R
+++ b/code/script/molecular_phenotypes/QC/bulk_expression_QC.R
@@ -52,10 +52,9 @@ if (is.null(opt[["tpm-gct"]])) stop("--tpm-gct is required")
 
 dir.create(opt$cwd, showWarnings = FALSE, recursive = TRUE)
 
-normalize_output_prefix <- function(path) {
-  stem <- sub("\\.(gct|GCT)(\\.gz)?$", "", basename(path))
-  stem <- sub("\\.gene_tpm$", "", stem)
-  stem <- sub("\\.tpm$", "", stem)
+normalize_output_prefix <- function(path, n_ext = 3) {
+  stem <- basename(path)
+  for (i in seq_len(n_ext)) stem <- sub("\\.[^.]+$", "", stem)
   stem
 }