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Patch 2 #2

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Update README.md
Fang0828 May 28, 2018
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Fang0828 May 28, 2018
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16 changes: 8 additions & 8 deletions README.md
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Expand Up @@ -15,21 +15,21 @@ 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
=====
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;

Expand All @@ -39,15 +39,15 @@ 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.

(2) allelic read counts of mutation from RNA-seq inlcuding 7 cloumns: chromosome (start from "chr"),
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),
Expand All @@ -68,14 +68,14 @@ 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!


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