From 4aaeeba8d4060d1993727c3e586dd07e2bed85d4 Mon Sep 17 00:00:00 2001 From: Fang Wang Date: Tue, 31 Jul 2018 12:26:32 -0500 Subject: [PATCH] Texomer version --- README.md | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 47c8335..89c0878 100644 --- a/README.md +++ b/README.md @@ -8,10 +8,9 @@ Draft date: Feb. 12, 2018 Description =========== -Texomer is a tool used in cancer genomic studies to discover single nucleotide variants (both somatic and germline) -with differential allelic cis-regulatory effects (DACRE) through an integration of whole-exome sequencing (WES) data and whole transcriptome sequencing (WTS) data. +Texomer is a tool used in cancer genomic studies to perform allele-specific, tumor-deconvoluted transcriptome-exome integration of the bulk whole exome (WES) and whole transcriptome sequencing (WTS) data obtained from autologous patient tissue sample. -It reports estimations of tumor purity at both the DNA and RNA level as well as intratumor heterogeneity at the DNA level. Moreover, Texomer yields allelic specific copy numbers and expression levels along with a DACRE (functional) score of each variant allele. +It reports estimations of tumor purity at both the DNA and RNA level as well as intratumor heterogeneity at the DNA level. Moreover, Texomer yeilds allelic specific copy numbers and expression levels along with a differential allelic cis-regulatory effect (DACRE) score of each variant allele. If the input only includes information at the DNA level, it only reports the estimates at the DNA level and focuses on somatic mutations. @@ -30,8 +29,8 @@ Installation ============ Please download and copy the distribution to your specific location. If you are cloning from github, ensure that you have git-lfs installed. -For example, if the downloaded distribuition is Texomer.tar.gz. - Type 'tar zxvf Texomer.tar.gz' +For example, if the downloaded distribuition is Texomer-1.0.tar.gz. + Type 'tar zxvf Texomer-1.0.tar.gz' Then, run Texomer.py in the resulting folder. @@ -42,7 +41,7 @@ Options: --version show program's version number and exit -h, --help Show this help message and exit. -p RSCRIPT, --Rscript=RSCRIPT - the path of DACRE + the path of Texomer -g GERMLINE, --germline=GERMLINE You can input your own germline mutation file if no -v. The file name of germline input file include 8