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YichaoOU · May 12, 2021 · 60f2a46 · 60f2a46
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diff --git a/docs/content/Differential_analysis/run_deseq2.rst b/docs/content/Differential_analysis/run_deseq2.rst
@@ -82,3 +82,12 @@ Output name by default is treatment.vs.control, folder is created, and DESEQ2 ra
 	HBBP1_VHL.vs.HBBP1_NT.plotDispEsts.pdf  HBBP1_VHL.vs.HBBP1_NT.R
 	HBBP1_VHL.vs.HBBP1_NT.cooks_distance.pdf  HBBP1_VHL.vs.HBBP1_NT.plotMA.pdf
 	HBBP1_VHL.vs.HBBP1_NT.deseq2_result.tsv   HBBP1_VHL.vs.HBBP1_NT.pvalue_hist.pdf
+
+
+Convert deseq2 result to bw files for visualization
+^^^^^^^^^^
+
+::
+
+	bdg_to_bw.py -f HBBP1.deseq2_result.tsv --data_frame -j HBBP1_bw_files
+	bdg_to_bw.py -f BGLT3.deseq2_result.tsv --data_frame -j BGLT3_bw_files
diff --git a/docs/content/NGS_pipelines/capturec.rst b/docs/content/NGS_pipelines/capturec.rst
@@ -99,6 +99,13 @@ To make a list of dpnII cut sites:
 
 	bedtools complement -i DpnII.bed -g ../bowtie_1.2.2_CapC_index/hg19_20copy_sizes.txt > DpnII_fragments.bed
 
+Differential analysis or data normalization
+^^^^^^^^^^^^^
+
+The pipeline output ``DESEQ2.input.tsv`` in jid folder.
+
+You can use it as the input for DESEQ2 pipeline. :doc:`run_DESEQ2.py <../Differential_analysis/run_deseq2>`
+
 Reference
 ^^^^^^^^^