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YichaoOU · May 12, 2021 · e97ba99 · e97ba99
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diff --git a/docs/content/Notes/ATAC.rst b/docs/content/Notes/ATAC.rst
@@ -13,6 +13,22 @@ I was suprised by this and checked TF-chip-seq data in Hudep2, for BCL11A, GATA1
 
 
 
+raw TN5 cut freq from pyDNase
+^^^^^^^^^^^^^^^^^^
+
+.. code:: bash
+
+	module load conda3
+
+	source activate /home/yli11/.conda/envs/pydnase
+
+	cd /home/yli11/Pipelines/example_NGS_data/atac_seq/atac_seq_yli11_2021-02-13/bam_files
+
+	dnase_wig_tracks.py -A test.bed 1631312_RFA007.rmdup.uq.bam fw.bdg rev.bdg
+
+fw.bdg and rev.bdg contains the Tn5 cut count.
+
+ref: https://pythonhosted.org/pyDNase/scripts.html?highlight=atac#dnase-wig-tracks-py
 
 reference
 ^^^^^^^^

diff --git a/...ooks/ggplot with custom p-value bar.ipynb → ...ooks/ggplot_with_custom_p-value_bar.ipynb b/...ooks/ggplot with custom p-value bar.ipynb → ...ooks/ggplot_with_custom_p-value_bar.ipynb
@@ -118,4 +118,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}
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@@ Expand Up / @@ -118,4 +118,4 @@ @@
      },
      "nbformat": 4,
      "nbformat_minor": 2
-    }
+    }