From 05c6cfd0f9ce8e89739f36c31e1e0374e82538cc Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 18 Mar 2020 13:41:25 -0500
Subject: [PATCH] Update README.md

---
 README.md | 36 ++++++++++++++++++------------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/README.md b/README.md
index e546867..60f4dc4 100644
--- a/README.md
+++ b/README.md
@@ -66,23 +66,23 @@ All dta available from NCBI’s Gene Expression Omnibus [@url:https://www.ncbi.n
 
 - Compute TFSEE to identify cognate transcription factors are under 'analysis'
  * Applicable to either enhancer method:
-  * Get H3K4me3 peaks: h3k4me3_processing.sh
-  * Get H3K27ac peaks: h3k27ac_processing.sh
-  * Get H3K4me1 peaks: h3k4me1_processing.sh
-  * Exclude regions based on H3K4me3 and promoters: excluded_regions_processing.sh
-  * RNA-seq analysis: RNA-seq_star.sh
-  * FPKM processing RNA-seq: rnaseq_processing.sh
+    * Get H3K4me3 peaks: h3k4me3_processing.sh
+    * Get H3K27ac peaks: h3k27ac_processing.sh
+    * Get H3K4me1 peaks: h3k4me1_processing.sh
+    * Exclude regions based on H3K4me3 and promoters: excluded_regions_processing.sh
+    * RNA-seq analysis: RNA-seq_star.sh
+    * FPKM processing RNA-seq: rnaseq_processing.sh
  * TFSEE using GRO-seq:
-  * Tune GroHMM: tune-hmm.sh
-  * Call Transcripts: call-transcripts.sh
-  * Make universe of Enhancers: groseq_processing.sh
-   * GRO_seq_TFSEE:
-     * TFSEE pre-processing: tfsee_processing.sh
-     * TFSEE score integration: matrix_analysis.py
-     * Rank order TF's clusters: rank_order.py
+      * Tune GroHMM: tune-hmm.sh
+      * Call Transcripts: call-transcripts.sh
+      * Make universe of Enhancers: groseq_processing.sh
+      * GRO_seq_TFSEE:
+         * TFSEE pre-processing: tfsee_processing.sh
+         * TFSEE score integration: matrix_analysis.py
+         * Rank order TF's clusters: rank_order.py
  * TFSEE using histone modifications ChIP-seq:
-  * Make universe of Enhancers: histone_centered_processing.sh
-   * Histone_TFSEE:
-     * TFSEE pre-processing: tfsee_processing.sh
-     * TFSEE score integration: matrix_analysis.py
-     * Rank order TF's clusters: rank_order.py
+      * Make universe of Enhancers: histone_centered_processing.sh
+      * Histone_TFSEE:
+         * TFSEE pre-processing: tfsee_processing.sh
+         * TFSEE score integration: matrix_analysis.py
+         * Rank order TF's clusters: rank_order.py
-- 
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