From 8a0ab2f028cac94abfe65420d296fd9935164f17 Mon Sep 17 00:00:00 2001
From: Fang0828 <38769725+Fang0828@users.noreply.github.com>
Date: Mon, 28 May 2018 14:25:02 -0500
Subject: [PATCH 1/2] Update README.md

---
 README.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 4ad0453..ef95e1c 100755
--- a/README.md
+++ b/README.md
@@ -15,14 +15,14 @@ focused on somatic mutaions.
 System requirements and dependency
 ==================================
 DACRE-scan runs on a x86_64 Linux system. It depends on samtools and bedtools to extract reads of variants from WTS data, R(version >= 3.2)
-for DACRE running which depends on R package bbmle, emdbook, copynumber,TitanCNA, facets, mixtools, ASCAT and Sequenza. I have already put R packeages 
+for DACRE-scan running which depends on R package bbmle, emdbook, copynumber,TitanCNA, facets, mixtools, ASCAT and Sequenza. I have already put R packeages 
 in the release, You can run DACRE-scan directly.
 
 Installation
 ============
 Please download and copy the distribution to your specific location. For example, the downloaded distribuition is DACRE_scan.tar.gz.
 	Type 'tar zxvf DACRE_scan.tar.gz'
-Then, run SNVexpress.py in DACRE_scan folder.
+Then, run DACRE_scan.py in DACRE_scan folder.
 
 Usage
 =====
@@ -39,7 +39,7 @@ DNA input files:
 	read counts in normal, ref and alt allelic read counts in tumor with header and tab separate.
 
 RNA input files:
-	two kinds of input files were allowed in ARDE:
+	two kinds of input files were allowed in DACRE_scan:
 
 	(1) bam file from RNA-seq. Load samtools and bedtools first if you input bam file.
 
@@ -47,7 +47,7 @@ RNA input files:
 	positive, reference allele, alternative allele, reference and alternative allelic read count from
 	RNA-seq, type of mutation (germline or somatic) with header and tab separate.    
 
-Output file: Multiple files would be output. If you input RNA file, ARDE would output both at DNA and RNA level. otherwise, it 
+Output file: Multiple files would be output. If you input RNA file, DACRE_scan would output both at DNA and RNA level. otherwise, it 
 	would output estimation at DNA level. 
 
 	(1) .segment file: position of segmentation; allele-specific copy number (Dmajor and Dminor), 
@@ -78,4 +78,4 @@ your feedback!
 
 Example
 =====
-python SNVexpress.py -g TCGA-3C-AAAU-01A-11D-A41F-09.snp.germline.input -s TCGA-3C-AAAU-10A-01D-A41F-09.mutect.vcf -e TCGA-3C-AAAU.RNA.SNV -p segACN
+python DACRE_scan.py -g TCGA-3C-AAAU-01A-11D-A41F-09.snp.germline.input -s TCGA-3C-AAAU-10A-01D-A41F-09.mutect.vcf -e TCGA-3C-AAAU.RNA.SNV -p segACN

From 7ce196f3bb3cfac689444705c7a296726eeb35ff Mon Sep 17 00:00:00 2001
From: Fang0828 <38769725+Fang0828@users.noreply.github.com>
Date: Mon, 28 May 2018 14:37:07 -0500
Subject: [PATCH 2/2] Update README.md

---
 README.md | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index ef95e1c..1ed3ce4 100755
--- a/README.md
+++ b/README.md
@@ -29,7 +29,7 @@ Usage
 Input files: 
 
 DNA input files: 
-	two kinds of input files were allowed in DACRE_scan:
+	two kinds of input files were allowed in DACRE-scan:
 
 	(1) input the output of varscan including germline and somatic mutations through -v;
 
@@ -39,7 +39,7 @@ DNA input files:
 	read counts in normal, ref and alt allelic read counts in tumor with header and tab separate.
 
 RNA input files:
-	two kinds of input files were allowed in DACRE_scan:
+	two kinds of input files were allowed in DACRE-scan:
 
 	(1) bam file from RNA-seq. Load samtools and bedtools first if you input bam file.
 
@@ -47,7 +47,7 @@ RNA input files:
 	positive, reference allele, alternative allele, reference and alternative allelic read count from
 	RNA-seq, type of mutation (germline or somatic) with header and tab separate.    
 
-Output file: Multiple files would be output. If you input RNA file, DACRE_scan would output both at DNA and RNA level. otherwise, it 
+Output file: Multiple files would be output. If you input RNA file, DACRE-scan would output both at DNA and RNA level. otherwise, it 
 	would output estimation at DNA level. 
 
 	(1) .segment file: position of segmentation; allele-specific copy number (Dmajor and Dminor), 
@@ -68,11 +68,11 @@ Python DACRE_scan.py –p Rscript/path –g germline.input –s somatic.input 
 
 About the default parameters
 ========================
-DACRE_scan optimizes estimation of purity and allele specific copy number through combing somatic mutation. So default -t is 1 corresponding to do the optimized iteration.
+DACRE-scan optimizes estimation of purity and allele specific copy number through combing somatic mutation. So default -t is 1 corresponding to do the optimized iteration.
 
 You can set -t 0 if you don't want to do optimization.
 
-Thank you very much for testing and using DACRE_scan. We appreciate so much for
+Thank you very much for testing and using DACRE-scan. We appreciate so much for
 your feedback!