StatFunGen · gaow · Feb 13, 2026 · Dec 4, 2025 · Dec 4, 2025 · Dec 4, 2025
diff --git a/code/molecular_phenotypes/QC/kellis_atacseq_preprocessing.ipynb b/code/molecular_phenotypes/QC/kellis_atacseq_preprocessing.ipynb
diff --git a/code/molecular_phenotypes/QC/xiong_atacseq_preprocessing.ipynb b/code/molecular_phenotypes/QC/xiong_atacseq_preprocessing.ipynb
diff --git a/code/reference_data/reference_data_preparation.ipynb b/code/reference_data/reference_data_preparation.ipynb
@@ -934,7 +934,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "id": "disturbed-understanding",
    "metadata": {
     "kernel": "SoS"
@@ -1168,7 +1168,7 @@
     "output: f'{_input:n}{\".collapse_only\" if stranded else \"\"}.gene.gtf'\n",
     "task: trunk_workers = 1, trunk_size = job_size, walltime = walltime, mem = mem, tags = f'{step_name}_{_output:bn}'\n",
     "bash: expand = \"${ }\", stderr = f'{_output}.stderr', stdout = f'{_output}.stdout', container = container, entrypoint = entrypoint\n",
-    "    collapse_annotation ${\"--collapse_only\" if stranded else \"\"} ${_input} ${_output}"
+    "    collapse_annotation.py ${\"--collapse_only\" if stranded else \"\"} ${_input} ${_output}"
    ]
   },
   {

diff --git a/website/_toc.yml b/website/_toc.yml
@@ -9,7 +9,7 @@ parts:
     - file: code/xqtl_protocol_demo.ipynb
   - caption: Command Generator
     chapters:
-    - file: code/commands_generator/bulk_expression_commands.ipynb
+  #  - file: code/commands_generator/bulk_expression_commands.ipynb #outdated
     - file: code/commands_generator/eQTL_analysis_commands.ipynb
   - caption: Reference data
     chapters:

diff --git a/website/nature_protocol/Figure_3/Figure_data/Figure_3_other_finemapping.rds b/website/nature_protocol/Figure_3/Figure_data/Figure_3_other_finemapping.rds
diff --git a/website/nature_protocol/Figure_3/Figure_data/README.md b/website/nature_protocol/Figure_3/Figure_data/README.md
@@ -0,0 +1 @@
+
diff --git a/website/nature_protocol/Figure_3/README.md b/website/nature_protocol/Figure_3/README.md
@@ -0,0 +1 @@
+
diff --git a/website/nature_protocol/Figure_3/fig3_other_finemapping.ipynb b/website/nature_protocol/Figure_3/fig3_other_finemapping.ipynb